Using RNA-guided FokI nucleases (RFNs) to increase specificity for RNA-guided genome editing

ABSTRACT

Many studies have shown that CRISPR-Cas nucleases can tolerate up to five mismatches and still cleave; it is hard to predict the effects of any given single or combination of mismatches on activity. Taken together, these nucleases can show significant off-target effects but it can be challenging to predict these sites. Described herein are methods for increasing the specificity of genome editing using the CRISPR/Cas system, e.g., using RNA-guided FokI Nucleases (RFNs), e.g., FokI-Cas9 or FokI-dCas9-based fusion proteins.

CLAIM OF PRIORITY

This application claims priority under 35 USC § 119(e) to U.S. PatentApplication Ser. Nos. 61/838,178, filed on Jun. 21, 2013; 61/838,148,filed on Jun. 21, 2013; 61/921,007, filed on Dec. 26, 2013; andPCT/US2014/028630, filed Mar. 14, 2014. The entire contents of theforegoing are hereby incorporated by reference.

FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with Government support under Grant Nos. DP1GM105378 awarded by the National Institutes of Health. The Governmenthas certain rights in the invention.

SEQUENCE LISTING

The contents of the electronic sequence listing created on Jan. 24,2020, named SequenceListing.txt and 182329 bytes in size, is herebyincorporated by reference in its entirety.

TECHNICAL FIELD

Methods for increasing specificity of RNA-guided genome editing, e.g.,editing using CRISPR/Cas9 systems, using RNA-guided FokI Nucleases(RFNs), e.g., FokI-dCas9 fusion proteins.

BACKGROUND

Recent work has demonstrated that clustered, regularly interspaced,short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems(Wiedenheft et al., Nature 482, 331-338 (2012); Horvath et al., Science327, 167-170 (2010); Terns et al., Curr Opin Microbiol 14, 321-327(2011)) can serve as the basis genome editing in bacteria, yeast andhuman cells, as well as in vivo in whole organisms such as fruit flies,zebrafish and mice (Wang et al., Cell 153, 910-918 (2013); Shen et al.,Cell Res (2013); Dicarlo et al., Nucleic Acids Res (2013); Jiang et al.,Nat Biotechnol 31, 233-239 (2013); Jinek et al., Elife 2, e00471 (2013);Hwang et al., Nat Biotechnol 31, 227-229 (2013); Cong et al., Science339, 819-823 (2013); Mali et al., Science 339, 823-826 (2013c); Cho etal., Nat Biotechnol 31, 230-232 (2013); Gratz et al., Genetics194(4):1029-35 (2013)). The Cas9 nuclease from S. pyogenes (hereaftersimply Cas9) can be guided via base pair complementarity between thefirst 20 nucleotides of an engineered gRNA and the complementary strandof a target genomic DNA sequence of interest that lies next to aprotospacer adjacent motif (PAM), e.g., a PAM matching the sequence NGGor NAG (Shen et al., Cell Res (2013); Dicarlo et al., Nucleic Acids Res(2013); Jiang et al., Nat Biotechnol 31, 233-239 (2013); Jinek et al.,Elife 2, e00471 (2013); Hwang et al., Nat Biotechnol 31, 227-229 (2013);Cong et al., Science 339, 819-823 (2013); Mali et al., Science 339,823-826 (2013c); Cho et al., Nat Biotechnol 31, 230-232 (2013); Jinek etal., Science 337, 816-821 (2012)). Previous studies performed in vitro(Jinek et al., Science 337, 816-821 (2012)), in bacteria (Jiang et al.,Nat Biotechnol 31, 233-239 (2013)) and in human cells (Cong et al.,Science 339, 819-823 (2013)) have shown that Cas9-mediated cleavage can,in some cases, be abolished by single mismatches at the gRNA/target siteinterface, particularly in the last 10-12 nucleotides (nts) located inthe 3′ end of the 20 nucleotide (nt) gRNA complementarity region.

SUMMARY

Many studies have shown that CRISPR-Cas nucleases can tolerate up tofive mismatches and still cleave; it is hard to predict the effects ofany given single or combination of mismatches on activity. Takentogether, these nucleases can show significant off-target effects but itcan be challenging to predict these sites. Described herein are methodsfor increasing the specificity of genome editing using the CRISPR/Cassystem, e.g., using RNA-guided FokI Nucleases (RFNs), e.g., FokI-Cas9 orFokI-dCas9-based fusion proteins.

In a first aspect, the invention provides FokI-dCas9 fusion proteins,comprising a FokI catalytic domain sequence fused to the terminus, e.g.,the N terminus, of dCas9, optionally with an intervening linker, e.g., alinker of from 2-30 amino acids, e.g., 4-12 amino acids, e.g., Gly₄Ser.In some embodiments, the FokI catalytic domain comprises amino acids388-583 or 408-583 of SEQ ID NO:4. In some embodiments, the dCas9comprises mutations at the dCas9 comprises mutations at D10, E762, H983,or D986; and at H840 or N863; e.g., at: (i) D10A or D10N; and (ii)H840A, H840Y or H840N.

In another aspect, the invention provides nucleic acids encoding thesefusion proteins, vector comprising the nucleic acids, and host cellsharboring or expressing the nucleic acids, vectors, or fusion proteins.

In another aspect, the invention provides methods for inducing asequence-specific break in a double-stranded DNA molecule, e.g., in agenomic sequence in a cell, the method comprising expressing in thecell, or contacting the cell with, the FokI-dCas9 fusion proteindescribed herein, and:

(a) two single guide RNAs, wherein each of the two single guide RNAsinclude sequences that are each complementary to one strand of thetarget sequence such that using both guide RNAs results in targetingboth strands (i.e., one single guide RNA targets a first strand, and theother guide RNA targets the complementary strand), and FokI cuts eachstrand resulting in a pair of nicks on opposite DNA strands, therebycreating a double-stranded break, or

(b) a tracrRNA and two crRNAs wherein each of the two crRNAs includesequences that are complementary to one strand of the target sequencesuch that using both crRNAs results in targeting both strands (i.e., onecrRNA targets a first strand, and the other crRNA targets thecomplementary strand), and FokI cuts each strand resulting in a pair ofnicks on opposite DNA strands, thereby creating a double-stranded break.

In another aspect, the invention provides methods for increasingspecificity of RNA-guided genome editing in a cell, the methodcomprising contacting the cell with an RNA-guided FokI Nuclease (RFN)fusion protein described herein.

The method may further comprise expressing in the cell, or contactingthe cell with, (a) two single guide RNAs, wherein each of the two singleguide RNAs include sequences that are each complementary to one strandof the target sequence such that using both guide RNAs results intargeting both strands (i.e., one single guide RNA targets a firststrand, and the other guide RNA targets the complementary strand), andFokI cuts each strand resulting in a pair of nicks on opposite DNAstrands, thereby creating a double-stranded break, or

(b) a tracrRNA and two crRNAs wherein each of the two crRNAs includesequences that are complementary to one strand of the target sequencesuch that using both crRNAs results in targeting both strands (i.e., onecrRNA targets a first strand, and the other crRNA targets thecomplementary strand), and FokI cuts each strand resulting in a pair ofnicks on opposite DNA strands, thereby creating a double-stranded break.

In some embodiments, the two target genomic sequences (i.e., thesequences to which the target complementarity regions of the crRNA orsingle guide RNAs are complementary) are spaced 10-20 base pairs apart,preferably 13-17 base pairs apart.

In some embodiments, an indel mutation is induced between the two targetsequences.

In some embodiments, the specificity of RNA-guided genome editing in acell is increased.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Methods and materials aredescribed herein for use in the present invention; other, suitablemethods and materials known in the art can also be used. The materials,methods, and examples are illustrative only and not intended to belimiting. All publications, patent applications, patents, sequences,database entries, and other references mentioned herein are incorporatedby reference in their entirety. In case of conflict, the presentspecification, including definitions, will control.

Other features and advantages of the invention will be apparent from thefollowing detailed description and figures, and from the claims.

DESCRIPTION OF DRAWINGS

FIG. 1: Schematic illustrating a gRNA/Cas9 nuclease complex bound to itstarget DNA site. Scissors indicate approximate cleavage points of theCas9 nuclease on the genomic DNA target site. Note the numbering ofnucleotides on the guide RNA proceeds in an inverse fashion from 5′ to3′.

FIG. 2A: Schematic illustrating the rationale for truncating the 5′complementarity region of a gRNA. Thick grey lines=target DNA site, thindark grey line structure=gRNA, grey oval=Cas9 nuclease, black linesindicate base pairing between gRNA and target DNA site.

FIG. 2B: Schematic overview of the EGFP disruption assay. Repair oftargeted Cas9-mediated double-stranded breaks in a single integratedEGFP-PEST reporter gene by error-prone NHEJ-mediated repair leads toframe-shift mutations that disrupt the coding sequence and associatedloss of fluorescence in cells.

FIGS. 2C-F: Activities of RGNs harboring sgRNAs bearing (C) singlemismatches, (D) adjacent double mismatches, (E) variably spaced doublemismatches, and (F) increasing numbers of adjacent mismatches assayed onthree different target sites in the EGFP reporter gene sequence. Meanactivities of replicates (see Online Methods) are shown, normalized tothe activity of a perfectly matched gRNA. Error bars indicate standarderrors of the mean. Positions mismatched in each gRNA are highlighted ingrey in the grid below. Sequences of the three EGFP target sites were asfollows:

EGFP Site 1 (SEQ ID NO: 1) GGGCACGGGCAGCTTGCCGGTGG EGFP Site 2(SEQ ID NO: 2) GATGCCGTTCTTCTGCTTGTCGG EGFP Site 3 (SEQ ID NO: 3)GGTGGTGCAGATGAACTTCAGGG

FIG. 2G: Mismatches at the 5′ end of the gRNA make CRISPR/Cas moresensitive more 3′ mismatches. The gRNAs Watson-Crick base pair betweenthe RNA&DNA with the exception of positions indicated with an “m” whichare mismatched using the Watson-Crick transversion (i.e. EGFP Site #2M18-19 is mismatched by changing the gRNA to its Watson-Crick partner atpositions 18 & 19. Although positions near the 5′ of the gRNA aregenerally very well tolerated, matches in these positions are importantfor nuclease activity when other residues are mismatched. When all fourpositions are mismatched, nuclease activity is no longer detectable.This further demonstrates that matches at these 5′ position can helpcompensate for mismatches at other more 3′ positions. Note theseexperiments were performed with a non-codon optimized version of Cas9which can show lower absolute levels of nuclease activity as compared tothe codon optimized version.

FIG. 2H: Efficiency of Cas9 nuclease activities directed by gRNAsbearing variable length complementarity regions ranging from 15 to 25nts in a human cell-based U2OS EGFP disruption assay. Expression of agRNA from the U6 promoter requires the presence of a 5′ G and thereforeit was only possible to evaluate gRNAs harboring certain lengths ofcomplementarity to the target DNA site (15, 17, 19, 20, 21, 23, and 25nts).

FIG. 3A: Efficiencies of EGFP disruption in human cells mediated by Cas9and full-length or shortened gRNAs for four target sites in the EGFPreporter gene. Lengths of complementarity regions and correspondingtarget DNA sites are shown. Ctrl=control gRNA lacking a complementarityregion.

FIG. 3B: Efficiencies of targeted indel mutations introduced at sevendifferent human endogenous gene targets by matched standard andtru-RGNs. Lengths of complementarity regions and corresponding targetDNA sites are shown. Indel frequencies were measured by T7EI assay.Ctrl=control gRNA lacking a complementarity region.

FIG. 3C: DNA sequences of indel mutations induced by RGNs using atru-gRNA or a matched full-length gRNA targeted to the EMX1 site. Theportion of the target DNA site that interacts with the gRNAcomplementarity region is highlighted in grey with the first base of thePAM sequence shown in lowercase. Deletions are indicated by dasheshighlighted in grey and insertions by italicized letters highlighted ingrey. The net number of bases deleted or inserted and the number oftimes each sequence was isolated are shown to the right.

FIG. 3D: Efficiencies of precise HDR/ssODN-mediated alterationsintroduced at two endogenous human genes by matched standard andtru-RGNs. % HDR was measured using a BamHI restriction digest assay (seethe Experimental Procedures for Example 2). Control gRNA=empty U6promoter vector.

FIG. 3E: U2OS.EGFP cells were transfected with variable amounts offull-length gRNA expression plasmids (top) or tru-gRNA expressionplasmids (bottom) together with a fixed amount of Cas9 expressionplasmid and then assayed for percentage of cells with decreased EGFPexpression. Mean values from duplicate experiments are shown withstandard errors of the mean. Note that the data obtained with tru-gRNAmatches closely with data from experiments performed with full-lengthgRNA expression plasmids instead of tru-gRNA plasmids for these threeEGFP target sites.

FIG. 3F: U2OS.EGFP cells were transfected with variable amount of Cas9expression plasmid together with variable amounts of full-length gRNAexpression plasmids (top) or tru-gRNA expression plasmids (bottom)(amounts determined for each tru-gRNA from the experiments of FIG. 3E).Mean values from duplicate experiments are shown with standard errors ofthe mean. Note that the data obtained with tru-gRNA matches closely withdata from experiments performed with full-length gRNA expressionplasmids instead of tru-gRNA plasmids for these three EGFP target sites.The results of these titrations determined the concentrations ofplasmids used in the EGFP disruption assays performed in Examples 1 and2.

FIGS. 4A-C. RNA-guided FokI nucleases and a CRISPR/Cas Subtype Ypestprotein 4 (Csy4)-based multiplex gRNA expression system.

(a) Schematic overview of RNA-guided FokI nucleases. Two FokI-dCas9fusion proteins are recruited to adjacent target sites by two differentgRNAs in order to facilitate FokI dimerization and DNA cleavage.

(b) Schematic overview of a Csy4-based multiplex gRNA expression system.Two gRNAs (with any 5′ end nucleotide) are co-expressed in a singletranscript from a U6 promoter with each gRNA flanked by Csy4 recognitionsites. Csy4 cleaves and releases gRNAs from the transcript. The Csy4recognition site remains at the 3′ end of the gRNA with a Csy4 nucleasebound to that site.

(c) Validation of the multiplex, Csy4-based system. Two gRNAs targetedto adjacent sites in EGFP were expressed in a single RNA transcriptusing the Csy4-based system in human U2OS.EGFP cells together with Csy4and Cas9 nucleases. Sequences of indel mutations induced in these cellsare shown. The wild-type sequence is shown in the top with both targetsites highlighted in grey and PAM sequences shown as underlined text.Deletions are indicated by dashes against gray background and insertionsby lowercase letters against a grey background. To the right of eachsequence, the sizes of insertions (+) or deletions (Δ) are specified.

FIGS. 5A-I. Design and optimization of RNA-guided FokI nucleases.

(a) Schematic illustrations of a ZFN, TALEN, FokI-dCas9 fusion, anddCas9-FokI fusion.

(b) Screening the EGFP disruption activities of FokI-dCas9 fusion withgRNA pairs targeted to half-sites in one of two orientations: PAMs in(left panel) and PAMs out (right panel). Half-sites were separated byspacer sequences of variable lengths ranging from 0 to 31 bps. EGFPdisruption was quantified by flow cytometry, n=1. Corresponding data forthe dCas9-FokI fusion and the same gRNA pairs is shown in FIG. 5E.

(c) Additional assessment of FokI-dCas9-mediated EGFP disruptionactivities on target sites with half-sites oriented with their PAMs outand with spacer lengths ranging from 10 to 20 bp. EGFP disruption wasquantified by flow cytometry. Error bars indicate standard errors of themean (s.e.m.), n=2.

(d) Mean EGFP disruption values of the data from (c) grouped accordingto spacer length. Error bars represent s.e.m.

(e) These plots show the results of a screen for dCas9-FokI activity inEGFP disruption assay in the U2OS.EGFP cells with 60 gRNA pairs withspacings of 0-31 bp and PAM in and PAM out orientations.

(f)-(i) Sequences of FokI-dCas9 induced mutations in U2OS cells areshown. The 23-nt target sequence bound by Cas9 or FokI-dCas9 is labeledin grey. The protospacer adjacent motif or PAM sequence is labeled inboldface with underlining. Deletions are marked with dashes on a lightgrey background. Insertions are highlighted in grey. The net number ofbases inserted or deleted are indicated in a column directly to theright of the sequences.

FIGS. 6A-D. Dimerization of FokI-dCas9 RFNs is required for efficientgenome editing activity.

(a) EGFP disruption activities of two RFN pairs assessed in the presenceof correctly targeted gRNA pairs (to EGFP sites 47 and 81) and pairs inwhich one or the other of the gRNAs has been replaced with another gRNAtargeted to a non-EGFP sequence (in the VEGFA gene). EGFP disruption wasquantified by flow cytometry. EGFP, Enhanced Green Fluorescent Protein;VEGFA, Vascular Endothelial Growth Factor A. Error bars representstandard errors of the mean (s.e.m.), n=3.

(b) Quantification of mutagenesis frequencies by T7EI assay performedwith genomic DNA from the same cells used in the EGFP disruption assayof (a). Error bars represent s.e.m., n=3.

(c) Activities of RFNs targeted to sites in the APC, MLH1 and VEGFAgenes. For each target, we co-expressed FokI-dCas9 with a pair ofcognate gRNAs, only one gRNA for the “left” half-site, or only one gRNAfor the “right” half-site. Rates of mutagenesis were measured by T7E1assay. APC, Adenomatous polyposis coli; MLH1, mutL homolog 1; VEGFA,Vascular Endothelial Growth Factor A. Error bars represent s.e.m., n=3.

(d) Mutagenesis frequencies of RFNs targeted to VEGFA site 1 at theon-target site and at five previously known off-target (OT) sites forone of the gRNAs used to target VEGFA site 1. Frequencies of mutationwere determined by deep sequencing. Each value reported was determinedfrom a single deep sequencing library prepared from genomic DNA pooledfrom three independent transfection experiments. The value shown for theon-target VEGFA site 1 (marked with an asterisk) is the same as the oneshown in FIG. 4a below and is only shown here for ease of comparisonwith the values presented in this figure.

FIGS. 7A-B. Mutagenic activities of a Cas9 nickase or FokI-dCas9co-expressed with a single gRNA.

(a) Indel mutation frequencies induced by FokI-dCas9 (left bars) or Cas9nickase (middle bars) in the presence of one or two gRNAs targeted tosix different human gene sites. For each gene target, we assessed indelfrequencies with both gRNAs, only one gRNA for the “left” half-site, oronly the other gRNA for the “right” half-site. Mutation frequencies weredetermined by deep sequencing. Each indel frequency value reported wasdetermined from a single deep sequencing library prepared from genomicDNA pooled from three independent transfection experiments. VEGFA,Vascular Endothelial Growth Factor A; DDB2, Damage-Specific DNA BindingProtein 2; FANCF, Fanconi Anemia, Complementation Group F; FES, FelineSarcoma Oncogene; RUNX 1, Runt-Related Transcription Factor 1.

(b) Data from (a) presented as a fold-reduction in the indel frequencycomparing values obtained for each target site with a gRNA pair to eachof the single gRNA experiments or to the control experiment (no gRNA andno Cas9 nickase or FokI-dCas9). This fold-reduction was calculated forboth FokI-dCas9 (left bars in each pair, lighter grey) and Cas9 nickase(right bars in each pair, darker grey).

FIGS. 8A-C: Single Cas9 nickases can introduce point mutations with highefficiencies into their target sites.

Frequencies of different point mutations found at each position inhalf-sites targeted by single gRNAs for (a) VEGFA, (b) FANCF, and (c)RUNX1 gene targets in the presence of FokI-dCas9, Cas9 nickase, or atdTomato control. Mutation frequencies were determined by deepsequencing. Each point mutation value reported was determined from asingle deep sequencing library prepared from genomic DNA pooled fromthree independent transfection experiments. Note that the genomic DNAused for these experiments was isolated from the same cells analyzed forindel mutations in FIGS. 7A-B. VEGFA, Vascular Endothelial Growth FactorA; FANCF, Fanconi Anemia, Complementation Group F; RUNX 1, Runt-RelatedTranscription Factor 1.

DETAILED DESCRIPTION

CRISPR RNA-guided nucleases (RGNs) have rapidly emerged as a facile andefficient platform for genome editing. Although Marraffini andcolleagues (Jiang et al., Nat Biotechnol 31, 233-239 (2013)) recentlyperformed a systematic investigation of Cas9 RGN specificity inbacteria, the specificities of RGNs in human cells have not beenextensively defined. Understanding the scope of RGN-mediated off-targeteffects in human and other eukaryotic cells will be critically essentialif these nucleases are to be used widely for research and therapeuticapplications. The present inventors have used a human cell-basedreporter assay to characterize off-target cleavage of Cas9-based RGNs.Single and double mismatches were tolerated to varying degrees dependingon their position along the guide RNA (gRNA)-DNA interface. Off-targetalterations induced by four out of six RGNs targeted to endogenous lociin human cells were readily detected by examination of partiallymismatched sites. The off-target sites identified harbor up to fivemismatches and many are mutagenized with frequencies comparable to (orhigher than) those observed at the intended on-target site. Thus RGNsare highly active even with imperfectly matched RNA-DNA interfaces inhuman cells, a finding that might confound their use in research andtherapeutic applications.

The results described herein reveal that predicting the specificityprofile of any given RGN is neither simple nor straightforward. The EGFPreporter assay experiments show that single and double mismatches canhave variable effects on RGN activity in human cells that do notstrictly depend upon their position(s) within the target site. Forexample, consistent with previously published reports, alterations inthe 3′ half of the gRNA/DNA interface generally have greater effectsthan those in the 5′ half (Jiang et al., Nat Biotechnol 31, 233-239(2013); Cong et al., Science 339, 819-823 (2013); Jinek et al., Science337, 816-821 (2012)); however, single and double mutations in the 3′ endsometimes also appear to be well tolerated whereas double mutations inthe 5′ end can greatly diminish activities. In addition, the magnitudeof these effects for mismatches at any given position(s) appears to besite-dependent. Comprehensive profiling of a large series of RGNs withtesting of all possible nucleotide substitutions (beyond theWatson-Crick transversions used in our EGFP reporter experiments) mayhelp provide additional insights into the range of potentialoff-targets. In this regard, the recently described bacterial cell-basedmethod of Marraffini and colleagues (Jiang et al., Nat Biotechnol 31,233-239 (2013)) or the in vitro, combinatorial library-based cleavagesite-selection methodologies previously applied to ZFNs by Liu andcolleagues (Pattanayak et al., Nat Methods 8, 765-770 (2011)) might beuseful for generating larger sets of RGN specificity profiles.

Despite these challenges in comprehensively predicting RGNspecificities, it was possible to identify bona fide off-targets of RGNsby examining a subset of genomic sites that differed from the on-targetsite by one to five mismatches. Notably, under conditions of theseexperiments, the frequencies of RGN-induced mutations at many of theseoff-target sites were similar to (or higher than) those observed at theintended on-target site, enabling the detection of mutations at thesesites using the T7EI assay (which, as performed in our laboratory, has areliable detection limit of ˜2 to 5% mutation frequency). Because thesemutation rates were very high, it was possible to avoid using deepsequencing methods previously required to detect much lower frequencyZFN- and TALEN-induced off-target alterations (Pattanayak et al., NatMethods 8, 765-770 (2011); Perez et al., Nat Biotechnol 26, 808-816(2008); Gabriel et al., Nat Biotechnol 29, 816-823 (2011); Hockemeyer etal., Nat Biotechnol 29, 731-734 (2011)). Analysis of RGN off-targetmutagenesis in human cells also confirmed the difficulties of predictingRGN specificities not all single and double mismatched off-target sitesshow evidence of mutation whereas some sites with as many as fivemismatches can also show alterations. Furthermore, the bona fideoff-target sites identified do not exhibit any obvious bias towardtransition or transversion differences relative to the intended targetsequence.

Although off-target sites were seen for a number of RGNs, identificationof these sites was neither comprehensive nor genome-wide in scale. Forthe six RGNs studied, only a very small subset of the much larger totalnumber of potential off-target sequences in the human genome wasexamined. Although examining such large numbers of loci for off-targetmutations by T7EI assay is neither a practical nor a cost-effectivestrategy, the use of high-throughput sequencing in future studies mightenable the interrogation of larger numbers of candidate off-target sitesand provide a more sensitive method for detecting bona fide off-targetmutations. For example, such an approach might enable the unveiling ofadditional off-target sites for the two RGNs for which we failed touncover any off-target mutations. In addition, an improved understandingboth of RGN specificities and of any epigenomic factors (e.g., DNAmethylation and chromatin status) that may influence RGN activities incells might also reduce the number of potential sites that need to beexamined and thereby make genome-wide assessments of RGN off-targetsmore practical and affordable.

A number of strategies can be used to minimize the frequencies ofgenomic off-target mutations. For example, the specific choice of RGNtarget site can be optimized; given that off-target sites that differ atup to five positions from the intended target site can be efficientlymutated by RGNs, choosing target sites with minimal numbers ofoff-target sites as judged by mismatch counting seems unlikely to beeffective; thousands of potential off-target sites that differ by fouror five positions within the 20 bp RNA:DNA complementarity region willtypically exist for any given RGN targeted to a sequence in the humangenome. It is also possible that the nucleotide content of the gRNAcomplementarity region might influence the range of potential off-targeteffects. For example, high GC-content has been shown to stabilizeRNA:DNA hybrids (Sugimoto et al., Biochemistry 34, 11211-11216 (1995))and therefore might also be expected to make gRNA/genomic DNAhybridization more stable and more tolerant to mismatches. Additionalexperiments with larger numbers of gRNAs will be needed to assess if andhow these two parameters (numbers of mismatched sites in the genome andstability of the RNA:DNA hybrid) influence the genome-wide specificitiesof RGNs. However, it is important to note that even if such predictiveparameters can be defined, the effect of implementing such guidelineswould be to further restrict the targeting range of RGNs.

One potential general strategy for reducing RGN-induced off-targeteffects might be to reduce the concentrations of gRNA and Cas9 nucleaseexpressed in the cell. This idea was tested using the RGNs for VEGFAtarget sites 2 and 3 in U2OS.EGFP cells; transfecting less gRNA- andCas9-expressing plasmid decreased the mutation rate at the on-targetsite but did not appreciably change the relative rates of off-targetmutations. Consistent with this, high-level off-target mutagenesis rateswere also observed in two other human cell types (HEK293 and K562 cells)even though the absolute rates of on-target mutagenesis are lower thanin U2OS.EGFP cells. Thus, reducing expression levels of gRNA and Cas9 incells is not likely to provide a solution for reducing off-targeteffects. Furthermore, these results also suggest that the high rates ofoff-target mutagenesis observed in human cells are not caused byoverexpression of gRNA and/or Cas9.

The finding that significant off-target mutagenesis can be induced byRGNs in three different human cell types has important implications forbroader use of this genome-editing platform. For research applications,the potentially confounding effects of high frequency off-targetmutations will need to be considered, particularly for experimentsinvolving either cultured cells or organisms with slow generation timesfor which the outcrossing of undesired alterations would be challenging.One way to control for such effects might be to utilize multiple RGNstargeted to different DNA sequences to induce the same genomicalteration because off-target effects are not random but instead relatedto the targeted site. However, for therapeutic applications, thesefindings clearly indicate that the specificities of RGNs will need to becarefully defined and/or improved if these nucleases are to be usedsafely in the longer term for treatment of human diseases.

Methods for Improving Specificity

As shown herein, CRISPR-Cas RNA-guided nucleases based on the S.pyogenes Cas9 protein can have significant off-target mutagenic effectsthat are comparable to or higher than the intended on-target activity(Example 1). Such off-target effects can be problematic for research andin particular for potential therapeutic applications. Therefore, methodsfor improving the specificity of CRISPR-Cas RNA guided nucleases (RGNs)are needed.

As described in Example 1, Cas9 RGNs can induce high-frequency indelmutations at off-target sites in human cells (see also Cradick et al.,2013; Fu et al., 2013; Hsu et al., 2013; Pattanayak et al., 2013). Theseundesired alterations can occur at genomic sequences that differ by asmany as five mismatches from the intended on-target site (see Example1). In addition, although mismatches at the 5′ end of the gRNAcomplementarity region are generally better tolerated than those at the3′ end, these associations are not absolute and showsite-to-site-dependence (see Example 1 and Fu et al., 2013; Hsu et al.,2013; Pattanayak et al., 2013). As a result, computational methods thatrely on the number and/or positions of mismatches currently have limitedpredictive value for identifying bona fide off-target sites. Therefore,methods for reducing the frequencies of off-target mutations remain animportant priority if RNA-guided nucleases are to be used for researchand therapeutic applications.

Dimerization is an attractive potential strategy for improving thespecificity of Cas9 nucleases. This is distinct from a paired Cas9nickase approach, which is not a true dimeric system. Paired nickaseswork by co-localizing two Cas9 nickases on a segment of DNA, therebyinducing high efficiency genome editing via an undefined mechanism.Because dimerization is not required for enzymatic activity, single Cas9nickases can also induce indels with high efficiencies at certain sites(via an unknown mechanism) and can therefore potentially cause unwantedoff-target mutations in the genome.

Thus, one strategy to improve the specificity of RGNs is fusing a FokIendonuclease domain to a catalytically inactive form of Cas9 bearing theD10A and H840A mutations (also known as dCas9). FokI nuclease domainfunctions as a dimer and therefore two subunits must be recruited to thesame local piece of DNA in order to induce a double-stranded break. Inthis configuration (FIG. 9A and Example 2), two FokI-dCas9 fusions arerecruited in an appropriate configuration using two different gRNAs toyield a double-stranded break. Thus, in this system, the FokI-dCas9fusions would bind to a site that is twice as long as that of a singleRGN and therefore this system would be expected to be more specific.

Therefore provided herein are FokI-dCas9 fusion proteins, wherein theFokI sequence is fused to dCas9 (preferably to the amino-terminal end ofdCas9, but also optionally to the carboxy terminus), optionally with anintervening linker, e.g., a linker of from 2-30 amino acids, e.g., 4-12amino acids, e.g., Gly₄Ser (SEQ ID NO:23) or (Gly₄Ser)₃. In someembodiments, the fusion proteins include a linker between the dCas9 andthe FokI domains. Linkers that can be used in these fusion proteins (orbetween fusion proteins in a concatenated structure) can include anysequence that does not interfere with the function of the fusionproteins. In preferred embodiments, the linkers are short, e.g., 2-20amino acids, and are typically flexible (i.e., comprising amino acidswith a high degree of freedom such as glycine, alanine, and serine). Insome embodiments, the linker comprises one or more units consisting ofGGGS (SEQ ID NO:22) or GGGGS (SEQ ID NO:23), e.g., two, three, four, ormore repeats of the GGGS (SEQ ID NO:22) or GGGGS (SEQ ID NO:23) unit.Other linker sequences can also be used.

Also described herein is a RNA-guided FokI nuclease platform in whichdimerization, rather than just co-localization, is required forefficient genome editing activity. These nucleases can robustly mediatehighly efficient genome editing in human cells and can reduce off-targetmutations to undetectable levels as judged by sensitive deep sequencingmethods. Also described is an efficient system for expressing pairs ofgRNAs with any 5′ end nucleotide, a method that confers a widertargeting range on the RFN platform. Finally, monomeric Cas9 nickasesgenerally introduce more undesirable indels and point mutations than thenucleases described herein in the presence of a single gRNA. Theseresults define a robust, user-friendly nuclease platform with thespecificity advantages of a well-characterized dimeric architecture andan improved mutagenesis profile relative to paired Cas9 nickases,features that will be important for research or therapeutic applicationsrequiring the highest possible genome editing precision.

Thus a new RNA-guided FokI Nuclease (RFN) platform is described hereinfor performing robust and highly specific genome editing in human cells.RFNs require two gRNAs for activity and function as dimers.Surprisingly, the engineering of an active RFN required fusion of theFokI nuclease domain to the amino-terminal end of the dCas9 protein, anarchitecture different from ZFNs and TALENs in which the FokI domain isfused to the carboxy-terminal end of engineered zinc finger ortranscription activator-like effector repeat arrays. RFNs also requirethat the half-sites bound by each Fok-dCas9/gRNA complex have aparticular relative orientation (PAMs out) with a relatively restrictedintervening spacer length of 14 to 17 bps (although activity may bepossible at additional spacings but with less consistent success).

The dimeric nature of RFNs provides important specificity advantagesrelative to standard monomeric Cas9 nucleases. In an ideal dimericsystem, little to no activity will be observed with monomers onhalf-sites. The present data demonstrate that FokI-dCas9 directed by asingle gRNA induces very little or no mutagenesis at RFN half-sites. 12single gRNAs (for six RFN target sites) were tested with co-expressedFokI-dCas9 and indels were observed at very low frequencies (range of0.0045% to 0.47%), in some cases at levels as low as background ratesobserved in control cells in which there was no expression of gRNA ornuclease. Given that the FokI nuclease domain functions as a dimer, itis presumed that any indels observed with a single gRNA are likely dueto recruitment of a FokI-dCas9 dimer to the DNA. Regardless ofmechanism, given that only very low level mutagenesis was observed whenFokI-dCas9 was tested with single gRNAs at 12 on-target half-sites, itis very unlikely that any mutagenesis will be induced at partiallymismatched, off-target half-sites. Indeed, an RFN targeted to VEGFA didnot induce detectable mutations at known off-target sites of one of thegRNAs as judged by deep sequencing.

Because RFNs are a true dimeric system, they possess a number ofimportant advantages over paired nickase technology, which depends onco-localization but does not require dimerization. First, the directcomparisons herein show that single Cas9 nickases generally induce indelmutations with greater efficiencies than do FokI-dCas9 fusion proteinsdirected by the same individual gRNAs. Second, monomeric Cas9 nickasescan also induce base pair substitutions in their target half-sites withhigh efficiencies, a previously unknown mutagenic side-effect that weuncovered in this study. Again, the direct comparisons show thatmonomeric Cas9 nickases induce these unwanted point mutations atsubstantially higher rates than FokI-dCas9 fusions guided by the samesingle gRNAs. Third, paired Cas9 nickases show greater promiscuity inthe orientation and spacing of target half-sites than dimeric RFNs andtherefore have a greater potential range of sites at which off-targetmutations might be induced. Paired nickase half-sites can be orientedwith their PAMs in or PAMs out and with spacer sequences ranging inlength from 0 to 1000 bps (Ran et al., Cell 154, 1380-1389 (2013); Maliet al., Nat Biotechnol 31,833-838 (2013); Cho et al., Genome Res(2013)). This promiscuity exists because the genome editing activitiesof Cas9 nickases do not depend on dimerization of the enzyme but ratherjust co-localization of the two nicks. By contrast, RFNs are much morestringent in their specificities—half-sites must have their PAMs out andmust be spaced apart by 14 to 17 bps, due to the requirement for twoappropriately positioned FokI cleavage domains for efficient cleavage.

FokI

FokI is a type IIs restriction endonuclease that includes a DNArecognition domain and a catalytic (endonuclease) domain. The fusionproteins described herein can include all of FokI or just the catalyticendonuclease domain, e.g., amino acids 388-583 or 408-583 of GenBankAcc. No. AAA24927.1, e.g., as described in Li et al., Nucleic Acids Res.39(1): 359-372 (2011); Cathomen and Joung, Mol. Ther. 16: 1200-1207(2008), or a mutated form of FokI as described in Miller et al. NatBiotechnol 25: 778-785 (2007); Szczepek et al., Nat Biotechnol 25:786-793 (2007); or Bitinaite et al., Proc. Natl. Acad. Sci. USA.95:10570-10575 (1998).

An exemplary amino acid sequence of FokI is as follows: (SEQ ID NO: 4)        10         20         30         40MFLSMVSKIR TFGWVQNPGK FENLKRVVQV FDRNSKVHNE        50         60         70         80VKNIKIPTLV KESKIQKELV AIMNQHDLIY TYKELVGTGT        90        100        110        120SIRSEAPCDA IIQATIADQG NKKGYIDNWS SDGFLRWAHA       130        140        150        160LGFIEYINKS DSFVITDVGL AYSKSADGSA IEKEILIEAI       170        180        190        200SSYPPAIRIL TLLEDGQHLT KFDLGKNLGF SGESGFTSLP       210        220        230        240EGILLDTLAN AMPKDKGEIR NNWEGSSDKY ARMIGGWLDK       250        260        270        280LGLVKQGKKE FIIPTLGKPD NKEFISHAFK ITGEGLKVLR       290        300        310        320RAKGSTKFTR VPKRVYWEML ATNLTDKEYV RTRRALILEI       330        340        350        360LIKAGSLKIE QIQDNLKKLG FDEVIETIEN DIKGLINTGI       370        380        390        400FIEIKGRFYQ LKDHILQFVI PNRGVTKQLV KSELEEKKSE       410        420        430        440LRHKLKYVPH EYIELIEIAR NSTQDRILEM KVMEFFMKVY       450        460        470        480GYRGKHLGGS RKPDGAIYTV GSPIDYGVIV DTKAYSGGYN       490        500        510        520LPIGQADEMQ RYVEENQTRN KHINPNEWWK VYPSSVTEFK       530        540        550        560FLFVSGHFKG NYKAQLTRLN HITNCNGAVL SVEELLIGGE        570        580MIKAGTLTLE EVRRKFNNGE INFAn exemplary nucleic acid sequence encoding FokI is as follows: (SEQ ID NO: 285) ATGTTTTTGAGTATGGTTTCTAAAATAAGAACTTTCGGTTGGGTTCAAAATCCAGGTAAATTTGAGAATTTAAAACGAGTAGTTCAAGTATTTGATAGAAATTCTAAAGTACATAATGAAGTGAAAAATATAAAGATACCAACCCTAGTCAAAGAAAGTAAGATCCAAAAAGAACTAGTTGCTATTATGAATCAACATGATTTGATTTATACATATAAAGAGTTAGTAGGAACAGGAACTTCAATACGTTCAGAAGCACCATGCGATGCAATTATTCAAGCAACAATAGCAGATCAAGGAAATAAAAAAGGCTATATCGATAATTGGTCATCTGACGGTTTTTTGCGTTGGGCACATGCTTTAGGATTTATTGAATATATAAATAAAAGTGATTCTTTTGTAATAACTGATGTTGGACTTGCTTACTCTAAATCAGCTGACGGCAGCGCCATTGAAAAAGAGATTTTGATTGAAGCGATATCATCTTATCCTCCAGCGATTCGTATTTTAACTTTGCTAGAAGATGGACAACATTTGACAAAGTTTGATCTTGGCAAGAATTTAGGTTTTAGTGGAGAAAGTGGATTTACTTCTCTACCGGAAGGAATTCTTTTAGATACTCTAGCTAATGCTATGCCTAAAGATAAAGGCGAAATTCGTAATAATTGGGAAGGATCTTCAGATAAGTACGCAAGAATGATAGGTGGTTGGCTGGATAAACTAGGATTAGTAAAGCAAGGAAAAAAAGAATTTATCATTCCTACTTTGGGTAAGCCGGACAATAAAGAGTTTATATCCCACGCTTTTAAAATTACTGGAGAAGGTTTGAAAGTACTGCGTCGAGCAAAAGGCTCTACAAAATTTACACGTGTACCTAAAAGAGTATATTGGGAAATGCTTGCTACAAACCTAACCGATAAAGAGTATGTAAGAACAAGAAGAGCTTTGATTTTAGAAATATTAATCAAAGCTGGATCATTAAAAATAGAACAAATACAAGACAACTTGAAGAAATTAGGATTTGATGAAGTTATAGAAACTATTGAAAATGATATCAAAGGCTTAATTAACACAGGTATATTTATAGAAATCAAAGGGCGATTTTATCAATTGAAAGACCATATTCTTCAATTTGTAATACCTAATCGTGGTGTGACTAAGCAACTAGTCAAAAGTGAACTGGAGGAGAAGAAATCTGAACTTCGTCATAAATTGAAATATGTGCCTCATGAATATATTGAATTAATTGAAATTGCCAGAAATTCCACTCAGGATAGAATTCTTGAAATGAAGGTAATGGAATTTTTTATGAAAGTTTATGGATATAGAGGTAAACATTTGGGTGGATCAAGGAAACCGGACGGAGCAATTTATACTGTCGGATCTCCTATTGATTACGGTGTGATCGTGGATACTAAAGCTTATAGCGGAGGTTATAATCTGCCAATTGGCCAAGCAGATGAAATGCAACGATATGTCGAAGAAAATCAAACACGAAACAAACATATCAACCCTAATGAATGGTGGAAAGTCTATCCATCTTCTGTAACGGAATTTAAGTTTTTATTTGTGAGTGGTCACTTTAAAGGAAACTACAAAGCTCAGCTTACACGATTAAATCATATCACTAATTGTAATGGAGCTGTTCTTAGTGTAGAAGAGCTTTTAATTGGTGGAGAAATGATTAAAGCCGGCACATTAACCTTAGAGGAAGTGAGACGGAAATTTAATAACGGCGAGATAAACTTTTAA

In some embodiments, the FokI nuclease used herein is at least about 50%identical SEQ ID NO:4, e.g., to amino acids 388-583 or 408-583 of SEQ IDNO:4. These variant nucleases must retain the ability to cleave DNA. Insome embodiments, the nucleotide sequences are about 50%, 55%, 60%, 65%,70%, 75%, 80%, 85%, 90%, 95%, 99% or 100% identical to amino acids388-583 or 408-583 of SEQ ID NO:4. In some embodiments, any differencesfrom amino acids 388-583 or 408-583 of SEQ ID NO:4 are in non-conservedregions.

To determine the percent identity of two sequences, the sequences arealigned for optimal comparison purposes (gaps are introduced in one orboth of a first and a second amino acid or nucleic acid sequence asrequired for optimal alignment, and non-homologous sequences can bedisregarded for comparison purposes). The length of a reference sequencealigned for comparison purposes is at least 50% (in some embodiments,about 50%, 55%, 60%, 65%, 70%, 75%, 85%, 90%, 95%, or 100% of the lengthof the reference sequence is aligned). The nucleotides or residues atcorresponding positions are then compared. When a position in the firstsequence is occupied by the same nucleotide or residue as thecorresponding position in the second sequence, then the molecules areidentical at that position. The percent identity between the twosequences is a function of the number of identical positions shared bythe sequences, taking into account the number of gaps, and the length ofeach gap, which need to be introduced for optimal alignment of the twosequences.

The comparison of sequences and determination of percent identitybetween two sequences can be accomplished using a mathematicalalgorithm. For purposes of the present application, the percent identitybetween two amino acid sequences is determined using the Needleman andWunsch ((1970) J. Mol. Biol. 48:444-453) algorithm which has beenincorporated into the GAP program in the GCG software package, using aBlossum 62 scoring matrix with a gap penalty of 12, a gap extend penaltyof 4, and a frameshift gap penalty of 5.

Cas9

A number of bacteria express Cas9 protein variants. The Cas9 fromStreptococcus pyogenes is presently the most commonly used; some of theother Cas9 proteins have high levels of sequence identity with the S.pyogenes Cas9 and use the same guide RNAs. Others are more diverse, usedifferent gRNAs, and recognize different PAM sequences as well (the 2-5nucleotide sequence specified by the protein which is adjacent to thesequence specified by the RNA). Chylinski et al. classified Cas9proteins from a large group of bacteria (RNA Biology 10:5, 1-12; 2013),and a large number of Cas9 proteins are listed in supplementary FIG. 1and supplementary table 1 thereof, which are incorporated by referenceherein. Additional Cas9 proteins are described in Esvelt et al., NatMethods. 2013 November; 10(11):1116-21 and Fonfara et al., “Phylogeny ofCas9 determines functional exchangeability of dual-RNA and Cas9 amongorthologous type II CRISPR-Cas systems.” Nucleic Acids Res. 2013 Nov.22. [Epub ahead of print] doi:10.1093/nar/gkt1074.

Cas9 molecules of a variety of species can be used in the methods andcompositions described herein. While the S. pyogenes and S. thermophilusCas9 molecules are the subject of much of the disclosure herein, Cas9molecules of, derived from, or based on the Cas9 proteins of otherspecies listed herein can be used as well. In other words, while themuch of the description herein uses S. pyogenes and S. thermophilus Cas9molecules, Cas9 molecules from the other species can replace them. Suchspecies include those set forth in the following table, which wascreated based on supplementary FIG. 1 of Chylinski et al., 2013.

Alternative Cas9 proteins GenBank Acc No. Bacterium 303229466Veillonella atypica ACS-134-V-Col7a 34762592 Fusobacterium nucleatumsubsp. vincentii 374307738 Filifactor alocis ATCC 35896 320528778Solobacterium moorei F0204 291520705 Coprococcus catus GD-7 42525843Treponema denticola ATCC 35405 304438954 Peptoniphilus duerdenii ATCCBAA-1640 224543312 Catenibacterium mitsuokai DSM 15897 24379809Streptococcus mutans UA159 15675041 Streptococcus pyogenes SF37016801805 Listeria innocua Clip11262 116628213 Streptococcus thermophilusLMD-9 323463801 Staphylococcus pseudintermedius ED99 352684361Acidaminococcus intestini RyC-MR95 302336020 Olsenella uli DSM 7084366983953 Oenococcus kitaharae DSM 17330 310286728 Bifidobacteriumbifidum S17 258509199 Lactobacillus rhamnosus GG 300361537 Lactobacillusgasseri JV-V03 169823755 Finegoldia magna ATCC 29328 47458868 Mycoplasmamobile 163K 284931710 Mycoplasma gallisepticum str. F 363542550Mycoplasma ovipneumoniae SC01 384393286 Mycoplasma canis PG 14 71894592Mycoplasma synoviae 53 238924075 Eubacterium rectale ATCC 33656116627542 Streptococcus thermophilus LMD-9 315149830 Enterococcusfaecalis TX0012 315659848 Staphylococcus lugdunensis M23590 160915782Eubacterium dolichum DSM 3991 336393381 Lactobacillus coryniformissubsp. torquens 310780384 Ilyobacter polytropus DSM 2926 325677756Ruminococcus albus 8 187736489 Akkermansia muciniphila ATCC BAA-835117929158 Acidothermus cellulolyticus 11B 189440764 Bifidobacteriumlongum DJO10A 283456135 Bifidobacterium dentium Bd1 38232678Corynebacterium diphtheriae NCTC 13129 187250660 Elusimicrobium minutumPei191 319957206 Nitratifractor salsuginis DSM 16511 325972003Sphaerochaeta globus str. Buddy 261414553 Fibrobacter succinogenessubsp. succinogenes 60683389 Bacteroides fragilis NCTC 9343 256819408Capnocytophaga ochracea DSM 7271 90425961 Rhodopseudomonas palustrisBisB18 373501184 Prevotella micans F0438 294674019 Prevotella ruminicola23 365959402 Flavobacterium columnare ATCC 49512 312879015 Aminomonaspaucivorans DSM 12260 83591793 Rhodospirillum rubrum ATCC 11170294086111 Candidatus Puniceispirillum marinum IMCC1322 121608211Verminephrobacter eiseniae EF01-2 344171927 Ralstonia syzygii R24159042956 Dinoroseobacter shibae DFL 12 288957741 Azospirillum sp- B51092109262 Nitrobacter hamburgensis X14 148255343 Bradyrhizobium sp- BTAi134557790 Wolinella succinogenes DSM 1740 218563121 Campylobacter jejunisubsp. jejuni 291276265 Helicobacter mustelae 12198 229113166 Bacilluscereus Rock1-15 222109285 Acidovorax ebreus TPSY 189485225 unculturedTermite group 1 182624245 Clostridium perfringens D str. 220930482Clostridium cellulolyticum H10 154250555 Parvibaculum lavamentivoransDS-1 257413184 Roseburia intestinalis L1-82 218767588 Neisseriameningitidis Z2491 15602992 Pasteurella multocida subsp. multocida319941583 Sutterella wadsworthensis 3 1 254447899 gamma proteobacteriumHTCC5015 54296138 Legionella pneumophila str. Paris 331001027Parasutterella excrementihominis YIT 11859 34557932 Wolinellasuccinogenes DSM 1740 118497352 Francisella novicida U112The constructs and methods described herein can include the use of anyof those Cas9 proteins, and their corresponding guide RNAs or otherguide RNAs that are compatible. The Cas9 from Streptococcus thermophilusLMD-9 CRISPR1 system has also been shown to function in human cells inCong et al (Science 339, 819 (2013)). Cas9 orthologs from N.meningitides are described in Hou et al., Proc Natl Acad Sci USA. 2013Sep. 24; 110(39):15644-9 and Esvelt et al., Nat Methods. 2013 November;10(11):1116-21. Additionally, Jinek et al. showed in vitro that Cas9orthologs from S. thermophilus and L. innocua, (but not from N.meningitidis or C. jejuni, which likely use a different guide RNA), canbe guided by a dual S. pyogenes gRNA to cleave target plasmid DNA,albeit with slightly decreased efficiency.

In some embodiments, the present system utilizes the Cas9 protein fromS. pyogenes, either as encoded in bacteria or codon-optimized forexpression in mammalian cells, containing mutations at D10, E762, H983,or D986 and H840 or N863, e.g., D10A/D10N and H840A/H840N/H840Y, torender the nuclease portion of the protein catalytically inactive;substitutions at these positions could be alanine (as they are inNishimasu al., Cell 156, 935-949 (2014)) or they could be otherresidues, e.g., glutamine, asparagine, tyrosine, serine, or aspartate,e.g., E762Q, H983N, H983Y, D986N, N863D, N863S, or N863H (FIG. 1C). Thesequence of the catalytically inactive S. pyogenes Cas9 that can be usedin the methods and compositions described herein is as follows; theexemplary mutations of D10A and H840A are in bold and underlined.

(SEQ ID NO: 5)         10         20         30         40 MDKKYSIGL A IGTNSVGWAV ITDEYKVPSK KFKVLGNTDR        50         60         70         80HSIKKNLIGA LLFDSGETAE ATRLKRTARR RYTRRKNRIC        90        100        110        120YLQEIFSNEM AKVDDSFFHR LEESFLVEED KKHERHPIFG       130        140        150        160NIVDEVAYHE KYPTIYHLRK KLVDSTDKAD LRLIYLALAH       170        180        190        200MIKFRGHFLI EGDLNPDNSD VDKLFIQLVQ TYNQLFEENP       210        220        230        240INASGVDAKA ILSARLSKSR RLENLIAQLP GEKKNGLFGN       250        260        270        280LIALSLGLTP NFKSNFDLAE DAKLQLSKDT YDDDLDNLLA       290        300        310        320QIGDQYADLF LAAKNLSDAI LLSDILRVNT EITKAPLSAS       330        340        350        360MIKRYDEHHQ DLTLLKALVR QQLPEKYKEI FFDQSKNGYA       370        380        390        400GYIDGGASQE EFYKFIKPIL EKMDGTEELL VKLNREDLLR       410        420        430        440KQRTFDNGSI PHQIHLGELH AILRRQEDFY PFLKDNREKI       450        460        470        480EKILTFRIPY YVGPLARGNS RFAWMTRKSE ETITPWNFEE       490        500        510        520VVDKGASAQS FIERMTNFDK NLPNEKVLPK HSLLYEYFTV       530        540        550        560YNELTKVKYV TEGMRKPAFL SGEQKKAIVD LLFKTNRKVT       570        580        590        600VKQLKEDYFK KIECFDSVEI SGVEDRFNAS LGTYHDLLKI       610        620        630        640IKDKDFLDNE ENEDILEDIV LTLTLFEDRE MIEERLKTYA       650        660        670        680HLFDDKVMKQ LKRRRYTGWG RLSRKLINGI RDKQSGKTIL       690        700        710        720DFLKSDGFAN RNFMQLIHDD SLTFKEDIQK AQVSGQGDSL       730        740        750        760HEHIANLAGS PAIKKGILQT VKVVDELVKV MGRHKPENIV       770        780        790        800IEMARENQTT QKGQKNSRER MKRIEEGIKE LGSQILKEHP       810        820        830        840VENTQLQNEK LYLYYLQNGR DMYVDQELDI NRLSDYDVD A       850        860        870        880IVPQSFLKDD SIDNKVLTRS DKNRGKSDNV PSEEVVKKMK       890        900        910        920NYWRQLLNAK LITQRKFDNL TKAERGGLSE LDKAGFIKRQ       930        940        950        960LVETRQITKH VAQILDSRMN TKYDENDKLI REVKVITLKS       970        980        990       1000KLVSDFRKDF QFYKVREINN YHHAHDAYLN AVVGTALIKK      1010       1020       1030       1040YPKLESEFVY GDYKVYDVRK MIAKSEQEIG KATAKYFFYS      1050       1060       1070       1080NIMNFFKTEI TLANGEIRKR PLIETNGETG EIVWDKGRDF      1090       1100       1110       1120ATVRKVLSMP QVNIVKKTEV QTGGFSKESI LPKRNSDKLI      1130       1140       1150       1160ARKKDWDPKK YGGFDSPTVA YSVLVVAKVE KGKSKKLKSV      1170       1180       1190       1200KELLGITIME RSSFEKNPID FLEAKGYKEV KKDLIIKLPK      1210       1220       1230       1240YSLFELENGR KRMLASAGEL QKGNELALPS KYVNFLYLAS      1250       1260       1270       1280HYEKLKGSPE DNEQKQLFVE QHKHYLDEII EQISEFSKRV      1290       1300       1310       1320ILADANLDKV LSAYNKHRDK PIREQAENII HLFTLTNLGA      1330       1340       1350       1360PAAFKYFDTT IDRKRYTSTK EVLDATLIHQ SITGLYETRI DLSQLGGD

In some embodiments, the Cas9 nuclease used herein is at least about 50%identical to the sequence of S. pyogenes Cas9, i.e., at least 50%identical to SEQ ID NO:5. In some embodiments, the nucleotide sequencesare about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or 100%identical to SEQ ID NO:5. In some embodiments, any differences from SEQID NO:5 are in non-conserved regions, as identified by sequencealignment of sequences set forth in Chylinski et al., RNA Biology 10:5,1-12; 2013 (e.g., in supplementary FIG. 1 and supplementary table 1thereof); Esvelt et al., Nat Methods. 2013 November; 10(11):1116-21 andFonfara et al., Nucl. Acids Res. (2014) 42 (4): 2577-2590. [Epub aheadof print 2013 Nov. 22] doi:10.1093/nar/gkt1074. Identity is determinedas set forth above.

Guide RNAs (gRNAs)

Guide RNAs generally speaking come in two different systems: System 1,which uses separate crRNA and tracrRNAs that function together to guidecleavage by Cas9, and System 2, which uses a chimeric crRNA-tracrRNAhybrid that combines the two separate guide RNAs in a single system(referred to as a single guide RNA or sgRNA, see also Jinek et al.,Science 2012; 337:816-821). The tracrRNA can be variably truncated and arange of lengths has been shown to function in both the separate system(system 1) and the chimeric gRNA system (system 2). For example, in someembodiments, tracrRNA may be truncated from its 3′ end by at least 1, 2,3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts. In someembodiments, the tracrRNA molecule may be truncated from its 5′ end byat least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts.Alternatively, the tracrRNA molecule may be truncated from both the 5′and 3′ end, e.g., by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15 or 20nts on the 5′ end and at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20,25, 30, 35 or 40 nts on the 3′ end. See, e.g., Jinek et al., Science2012; 337:816-821; Mali et al., Science. 2013 Feb. 15; 339(6121):823-6;Cong et al., Science. 2013 Feb. 15; 339(6121):819-23; and Hwang and Fuet al., Nat Biotechnol. 2013 March; 31(3):227-9; Jinek et al., Elife 2,e00471 (2013)). For System 2, generally the longer length chimeric gRNAshave shown greater on-target activity but the relative specificities ofthe various length gRNAs currently remain undefined and therefore it maybe desirable in certain instances to use shorter gRNAs. In someembodiments, the gRNAs are complementary to a region that is withinabout 100-800 bp upstream of the transcription start site, e.g., iswithin about 500 bp upstream of the transcription start site, includesthe transcription start site, or within about 100-800 bp, e.g., withinabout 500 bp, downstream of the transcription start site. In someembodiments, vectors (e.g., plasmids) encoding more than one gRNA areused, e.g., plasmids encoding, 2, 3, 4, 5, or more gRNAs directed todifferent sites in the same region of the target gene.

Cas9 nuclease can be guided to specific 17-20 nt genomic targets bearingan additional proximal protospacer adjacent motif (PAM), e.g., ofsequence NGQ using a guide RNA, e.g., a single gRNA or a tracrRNA/crRNA,bearing 17-20 nts at its 5′ end that are complementary to thecomplementary strand of the genomic DNA target site. Thus, the presentmethods can include the use of a single guide RNA comprising a crRNAfused to a normally trans-encoded tracrRNA, e.g., a single Cas9 guideRNA as described in Mali et al., Science 2013 Feb. 15; 339(6121):823-6,with a sequence at the 5′ end that is complementary to the targetsequence, e.g., of 25-17, optionally 20 or fewer nucleotides (nts),e.g., 20, 19, 18, or 17 nts, preferably 17 or 18 nts, of thecomplementary strand to a target sequence immediately 5′ of aprotospacer adjacent motif (PAM), e.g., NGG, NAG, or NNGG. In someembodiments, the single Cas9 guide RNA consists of the sequence:

(SEQ ID NO: 6) (X₁₇₋₂₀)GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCG(X_(N)); (SEQ ID NO: 7)(X₁₇₋₂₀)GUUUUAGAGCUAUGCUGAAAAGCAUAGCAAGUUAAAAUAAG GCUAGUCCGUUAUC(X_(N));(SEQ ID NO: 8) (X₁₇₋₂₀)GUUUUAGAGCUAUGCUGUUUUGGAAACAAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUC(X_(N)); (SEQ ID NO: 9)(X₁₇₋₂₀)GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC(X_(N)), (SEQ ID NO: 10)(X₁₇₋₂₀)GUUUAAGAGCUAGAAAUAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC; (SEQ ID NO: 11)(X₁₇₋₂₀)GUUUUAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC; or (SEQ ID NO: 12)(X₁₇₋₂₀)GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC;

wherein X₁₇₋₂₀ is the nucleotide sequence complementary to 17-20consecutive nucleotides of the target sequence. DNAs encoding the singleguide RNAs have been described previously in the literature (Jinek etal., Science. 337(6096):816-21 (2012) and Jinek et al., Elife. 2:e00471(2013)).

The guide RNAs can include X_(N) which can be any sequence, wherein N(in the RNA) can be 0-200, e.g., 0-100, 0-50, or 0-20, that does notinterfere with the binding of the ribonucleic acid to Cas9.

In some embodiments, the guide RNA includes one or more Adenine (A) orUracil (U) nucleotides on the 3′ end. In some embodiments the RNAincludes one or more U, e.g., 1 to 8 or more Us (e.g., U, UU, UUU, UUUU,UUUUU, UUUUUU, UUUUUUU, UUUUUUUU) at the 3′ end of the molecule, as aresult of the optional presence of one or more Ts used as a terminationsignal to terminate RNA PolIII transcription.

Although some of the examples described herein utilize a single gRNA,the methods can also be used with dual gRNAs (e.g., the crRNA andtracrRNA found in naturally occurring systems). In this case, a singletracrRNA would be used in conjunction with multiple different crRNAsexpressed using the present system, e.g., the following:

-   (X₁₇₋₂₀)GUUUUAGAGCUA (SEQ ID NO:13);-   (X₁₇₋₂₀)GUUUUAGAGCUAUGCUGUUUUG (SEQ ID NO:14); or-   (X₁₇₋₂₀)GUUUUAGAGCUAUGCU (SEQ ID NO:15); and a tracrRNA sequence. In    this case, the crRNA is used as the guide RNA in the methods and    molecules described herein, and the tracrRNA can be expressed from    the same or a different DNA molecule. In some embodiments, the    methods include contacting the cell with a tracrRNA comprising or    consisting of the sequence    GGAACCAUUCAAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUA    UCAACUUGAAAAAGUGGCACCGAGUCGGUGC (SEQ ID NO:16) or an active portion    thereof (an active portion is one that retains the ability to form    complexes with Cas9 or dCas9). In some embodiments, the tracrRNA    molecule may be truncated from its 3′ end by at least 1, 2, 3, 4, 5,    6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts. In another embodiment,    the tracrRNA molecule may be truncated from its 5′ end by at least    1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35 or 40 nts.    Alternatively, the tracrRNA molecule may be truncated from both the    5′ and 3′ end, e.g., by at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15    or 20 nts on the 5′ end and at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,    15, 20, 25, 30, 35 or 40 nts on the 3′ end. Exemplary tracrRNA    sequences in addition to SEQ ID NO:8 include the following:-   UAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCA CCGAGUCGGUGC (SEQ    ID NO:17) or an active portion thereof; or-   AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGU GGCACCGAGUCGGUGC    (SEQ ID NO:18) or an active portion thereof.

In some embodiments wherein (X₁₇₋₂₀)GUUUUAGAGCUAUGCUGUUUUG (SEQ IDNO:14) is used as a crRNA, the following tracrRNA is used:

-   GGAACCAUUCAAAACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUA    UCAACUUGAAAAAGUGGCACCGAGUCGGUGC (SEQ ID NO:16) or an active portion    thereof. In some embodiments wherein (X₁₇₋₂₀)GUUUUAGAGCUA (SEQ ID    NO:13) is used as a crRNA, the following tracrRNA is used:-   UAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCA CCGAGUCGGUGC (SEQ    ID NO:17) or an active portion thereof. In some embodiments wherein    (X₁₇₋₂₀)GUUUUAGAGCUAUGCU (SEQ ID NO:15) is used as a crRNA, the    following tracrRNA is used:-   AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGU GGCACCGAGUCGGUGC    (SEQ ID NO:18) or an active portion thereof.

In some embodiments, the gRNA is targeted to a site that is at leastthree or more mismatches different from any sequence in the rest of thegenome in order to minimize off-target effects.

Modified RNA oligonucleotides such as locked nucleic acids (LNAs) havebeen demonstrated to increase the specificity of RNA-DNA hybridizationby locking the modified oligonucleotides in a more favorable (stable)conformation. For example, 2′-O-methyl RNA is a modified base wherethere is an additional covalent linkage between the 2′ oxygen and 4′carbon which when incorporated into oligonucleotides can improve overallthermal stability and selectivity (Formula I).

Thus in some embodiments, the tru-gRNAs disclosed herein may compriseone or more modified RNA oligonucleotides. For example, the truncatedguide RNAs molecules described herein can have one, some or all of the17-18 or 17-19 nts 5′ region of the guide RNA complementary to thetarget sequence are modified, e.g., locked (2′-O-4′-C methylene bridge),5′-methylcytidine, 2′-O-methyl-pseudouridine, or in which the ribosephosphate backbone has been replaced by a polyamide chain (peptidenucleic acid), e.g., a synthetic ribonucleic acid.

In other embodiments, one, some or all of the nucleotides of thetru-gRNA sequence may be modified, e.g., locked (2′-O-4′-C methylenebridge), 5′-methylcytidine, 2′-O-methyl-pseudouridine, or in which theribose phosphate backbone has been replaced by a polyamide chain(peptide nucleic acid), e.g., a synthetic ribonucleic acid.

In some embodiments, the single guide RNAs and/or crRNAs and/ortracrRNAs can include one or more Adenine (A) or Uracil (U) nucleotideson the 3′ end.

Existing Cas9-based RGNs use gRNA-DNA heteroduplex formation to guidetargeting to genomic sites of interest. However, RNA-DNA heteroduplexescan form a more promiscuous range of structures than their DNA-DNAcounterparts. In effect, DNA-DNA duplexes are more sensitive tomismatches, suggesting that a DNA-guided nuclease may not bind asreadily to off-target sequences, making them comparatively more specificthan RNA-guided nucleases. Thus, the guide RNAs usable in the methodsdescribed herein can be hybrids, i.e., wherein one or moredeoxyribonucleotides, e.g., a short DNA oligonucleotide, replaces all orpart of the gRNA, e.g., all or part of the complementarity region of agRNA. This DNA-based molecule could replace either all or part of thegRNA in a single gRNA system or alternatively might replace all of partof the crRNA and/or tracrRNA in a dual crRNA/tracrRNA system. Such asystem that incorporates DNA into the complementarity region should morereliably target the intended genomic DNA sequences due to the generalintolerance of DNA-DNA duplexes to mismatching compared to RNA-DNAduplexes. Methods for making such duplexes are known in the art, See,e.g., Barker et al., BMC Genomics. 2005 Apr. 22; 6:57; and Sugimoto etal., Biochemistry. 2000 Sep. 19; 39(37):11270-81.

In addition, in a system that uses separate crRNA and tracrRNA, one orboth can be synthetic and include one or more modified (e.g., locked)nucleotides or deoxyribonucleotides.

In a cellular context, complexes of Cas9 with these synthetic gRNAscould be used to improve the genome-wide specificity of the CRISPR/Cas9nuclease system.

The methods described can include expressing in a cell, or contactingthe cell with, a Cas9 gRNA plus a fusion protein as described herein.

Expression Systems

In order to use the fusion proteins described, it may be desirable toexpress them from a nucleic acid that encodes them. This can beperformed in a variety of ways. For example, the nucleic acid encodingthe guide RNA can be cloned into an intermediate vector fortransformation into prokaryotic or eukaryotic cells for replicationand/or expression. Intermediate vectors are typically prokaryotevectors, e.g., plasmids, or shuttle vectors, or insect vectors, forstorage or manipulation of the nucleic acid encoding the fusion proteinsfor production of the fusion proteins. The nucleic acid encoding thefusion proteins can also be cloned into an expression vector, foradministration to a plant cell, animal cell, preferably a mammalian cellor a human cell, fungal cell, bacterial cell, or protozoan cell.

To obtain expression, a sequence encoding a fusion protein is typicallysubcloned into an expression vector that contains a promoter to directtranscription. Suitable bacterial and eukaryotic promoters are wellknown in the art and described, e.g., in Sambrook et al., MolecularCloning, A Laboratory Manual (3d ed. 2001); Kriegler, Gene Transfer andExpression: A Laboratory Manual (1990); and Current Protocols inMolecular Biology (Ausubel et al., eds., 2010). Bacterial expressionsystems for expressing the engineered protein are available in, e.g., E.coli, Bacillus sp., and Salmonella (Palva et al., 1983, Gene22:229-235). Kits for such expression systems are commerciallyavailable. Eukaryotic expression systems for mammalian cells, yeast, andinsect cells are well known in the art and are also commerciallyavailable.

The promoter used to direct expression of a nucleic acid depends on theparticular application. For example, a strong constitutive promoter istypically used for expression and purification of fusion proteins. Incontrast, when the guide RNA is to be administered in vivo for generegulation, either a constitutive or an inducible promoter can be used,depending on the particular use of the guide RNA. In addition, apreferred promoter for administration of the guide RNA can be a weakpromoter, such as HSV TK or a promoter having similar activity. Thepromoter can also include elements that are responsive totransactivation, e.g., hypoxia response elements, Gal4 responseelements, lac repressor response element, and small molecule controlsystems such as tetracycline-regulated systems and the RU-486 system(see, e.g., Gossen & Bujard, 1992, Proc. Natl. Acad. Sci. USA, 89:5547;Oligino et al., 1998, Gene Ther., 5:491-496; Wang et al., 1997, GeneTher., 4:432-441; Neering et al., 1996, Blood, 88:1147-55; and Rendahlet al., 1998, Nat. Biotechnol., 16:757-761).

In addition to the promoter, the expression vector typically contains atranscription unit or expression cassette that contains all theadditional elements required for the expression of the nucleic acid inhost cells, either prokaryotic or eukaryotic. A typical expressioncassette thus contains a promoter operably linked, e.g., to the nucleicacid sequence encoding the gRNA, and any signals required, e.g., forefficient polyadenylation of the transcript, transcriptionaltermination, ribosome binding sites, or translation termination.Additional elements of the cassette may include, e.g., enhancers, andheterologous spliced intronic signals.

The particular expression vector used to transport the geneticinformation into the cell is selected with regard to the intended use ofthe gRNA, e.g., expression in plants, animals, bacteria, fungus,protozoa, etc. Standard bacterial expression vectors include plasmidssuch as pBR322 based plasmids, pSKF, pET23D, and commercially availabletag-fusion expression systems such as GST and LacZ.

Expression vectors containing regulatory elements from eukaryoticviruses are often used in eukaryotic expression vectors, e.g., SV40vectors, papilloma virus vectors, and vectors derived from Epstein-Barrvirus. Other exemplary eukaryotic vectors include pMSG pAV009/A+,pMTO10/A+, pMAMneo-5, baculovirus pDSVE, and any other vector allowingexpression of proteins under the direction of the SV40 early promoter,SV40 late promoter, metallothionein promoter, murine mammary tumor viruspromoter, Rous sarcoma virus promoter, polyhedrin promoter, or otherpromoters shown effective for expression in eukaryotic cells.

The vectors for expressing the guide RNAs can include RNA Pol IIIpromoters to drive expression of the guide RNAs, e.g., the H1, U6 or 7SKpromoters. These human promoters allow for expression of gRNAs inmammalian cells following plasmid transfection. Alternatively, a T7promoter may be used, e.g., for in vitro transcription, and the RNA canbe transcribed in vitro and purified. Vectors suitable for theexpression of short RNAs, e.g., siRNAs, shRNAs, or other small RNAs, canbe used. With the Cys4-based multiplex system described in FIG. 4B,multiple gRNAs can be expressed in a single transcript (driven by a RNAPol II or Pol III promoter) and then cleaved out from that largertranscript.

Some expression systems have markers for selection of stably transfectedcell lines such as thymidine kinase, hygromycin B phosphotransferase,and dihydrofolate reductase. High yield expression systems are alsosuitable, such as using a baculovirus vector in insect cells, with thegRNA encoding sequence under the direction of the polyhedrin promoter orother strong baculovirus promoters.

The elements that are typically included in expression vectors alsoinclude a replicon that functions in E. coli, a gene encoding antibioticresistance to permit selection of bacteria that harbor recombinantplasmids, and unique restriction sites in nonessential regions of theplasmid to allow insertion of recombinant sequences.

Standard transfection methods are used to produce bacterial, mammalian,yeast or insect cell lines that express large quantities of protein,which are then purified using standard techniques (see, e.g., Colley etal., 1989, J. Biol. Chem., 264:17619-22; Guide to Protein Purification,in Methods in Enzymology, vol. 182 (Deutscher, ed., 1990)).Transformation of eukaryotic and prokaryotic cells are performedaccording to standard techniques (see, e.g., Morrison, 1977, J.Bacteriol. 132:349-351; Clark-Curtiss & Curtiss, Methods in Enzymology101:347-362 (Wu et al., eds, 1983).

Any of the known procedures for introducing foreign nucleotide sequencesinto host cells may be used. These include the use of calcium phosphatetransfection, polybrene, protoplast fusion, electroporation,nucleofection, liposomes, microinjection, naked DNA, plasmid vectors,viral vectors, both episomal and integrative, and any of the otherwell-known methods for introducing cloned genomic DNA, cDNA, syntheticDNA or other foreign genetic material into a host cell (see, e.g.,Sambrook et al., supra). It is only necessary that the particulargenetic engineering procedure used be capable of successfullyintroducing at least one gene into the host cell capable of expressingthe gRNA.

The present invention includes the vectors and cells comprising thevectors.

EXAMPLES

The invention is further described in the following examples, which donot limit the scope of the invention described in the claims.

Example 1. Assessing Specificity of RNA-Guided Endonucleases

CRISPR RNA-guided nucleases (RGNs) have rapidly emerged as a facile andefficient platform for genome editing. This example describes the use ofa human cell-based reporter assay to characterize off-target cleavage ofCas9-based RGNs.

Materials and Methods

The following materials and methods were used in Example 1.

Construction of Guide RNAs

DNA oligonucleotides harboring variable 20 nt sequences for Cas9targeting were annealed to generate short double-strand DNA fragmentswith 4 bp overhangs compatible with ligation into BsmBI-digested plasmidpMLM3636. Cloning of these annealed oligonucleotides generates plasmidsencoding a chimeric +103 single-chain guide RNA with 20 variable 5′nucleotides under expression of a U6 promoter (Hwang et al., NatBiotechnol 31, 227-229 (2013); Mali et al., Science 339, 823-826(2013)). pMLM3636 and the expression plasmid pJDS246 (encoding a codonoptimized version of Cas9) used in this study are both available throughthe non-profit plasmid distribution service Addgene(addgene.org/crispr-cas).

EGFP Activity Assays

U2OS.EGFP cells harboring a single integrated copy of an EGFP-PESTfusion gene were cultured as previously described (Reyon et al., NatBiotech 30, 460-465 (2012)). For transfections, 200,000 cells wereNucleofected with the indicated amounts of gRNA expression plasmid andpJDS246 together with 30 ng of a Td-tomato-encoding plasmid using the SECell Line 4D-Nucleofector™ X Kit (Lonza) according to the manufacturer'sprotocol. Cells were analyzed 2 days post-transfection using a BD LSRIIflow cytometer. Transfections for optimizing gRNA/Cas9 plasmidconcentration were performed in triplicate and all other transfectionswere performed in duplicate.

PCR Amplification and Sequence Verification of Endogenous Human GenomicSites

PCR reactions were performed using Phusion Hot Start II high-fidelityDNA polymerase (NEB). Most loci amplified successfully using touchdownPCR (98° C., 10 s; 72-62° C., 1° C./cycle, 15 s; 72° C., 30 s110 cycles,[98° C., 10 s; 62° C., 15 s; 72° C., 30 s]125 cycles). PCR for theremaining targets were performed with 35 cycles at a constant annealingtemperature of 68° C. or 72° C. and 3% DMSO or 1M betaine, if necessary.PCR products were analyzed on a QIAXCEL capillary electrophoresis systemto verify both size and purity. Validated products were treated withExoSap-IT (Affymetrix) and sequenced by the Sanger method (MGH DNASequencing Core) to verify each target site.

Determination of RGN-Induced On- and Off-Target Mutation Frequencies inHuman Cells

For U2OS.EGFP and K562 cells, 2×10⁵ cells were transfected with 250 ngof gRNA expression plasmid or an empty U6 promoter plasmid (for negativecontrols), 750 ng of Cas9 expression plasmid, and 30 ng of td-Tomatoexpression plasmid using the 4D Nucleofector System according to themanufacturer's instructions (Lonza). For HEK293 cells, 1.65×10⁵ cellswere transfected with 125 ng of gRNA expression plasmid or an empty U6promoter plasmid (for the negative control), 375 ng of Cas9 expressionplasmid, and 30 ng of a td-Tomato expression plasmid using LipofectamineLTX reagent according to the manufacturer's instructions (LifeTechnologies). Genomic DNA was harvested from transfected U2OS.EGFP,HEK293, or K562 cells using the QIAamp DNA Blood Mini Kit (QIAGEN),according to the manufacturer's instructions. To generate enough genomicDNA to amplify the off-target candidate sites, DNA from threeNucleofections (for U2OS.EGFP cells), two Nucleofections (for K562cells), or two Lipofectamine LTX transfections was pooled togetherbefore performing T7EI. This was done twice for each condition tested,thereby generating duplicate pools of genomic DNA representing a totalof four or six individual transfections. PCR was then performed usingthese genomic DNAs as templates as described above and purified usingAmpure XP beads (Agencourt) according to the manufacturer'sinstructions. T7EI assays were performed as previously described (Reyonet al., 2012, supra).

DNA Sequencing of NHEJ-Mediated Indel Mutations

Purified PCR products used for the T7EI assay were cloned into ZeroBlunt TOPO vector (Life Technologies) and plasmid DNAs were isolatedusing an alkaline lysis miniprep method by the MGH DNA Automation Core.Plasmids were sequenced using an M13 forward primer (5′ GTAAAACGACGGCCAG3′ (SEQ ID NO:19)) by the Sanger method (MGH DNA Sequencing Core).

Example 1a. Single Nucleotide Mismatches

To begin to define the specificity determinants of RGNs in human cells,a large-scale test was performed to assess the effects of systematicallymismatching various positions within multiple gRNA/target DNAinterfaces. To do this, a quantitative human cell-based enhanced greenfluorescent protein (EGFP) disruption assay previously described (seeMethods above and Reyon et al., 2012, supra) that enables rapidquantitation of targeted nuclease activities (FIG. 2B) was used. In thisassay, the activities of nucleases targeted to a single integrated EGFPreporter gene can be quantified by assessing loss of fluorescence signalin human U2OS.EGFP cells caused by inactivating frameshiftinsertion/deletion (indel) mutations introduced by error pronenon-homologous end-joining (NHEJ) repair of nuclease-induceddouble-stranded breaks (DSBs) (FIG. 2B). For the studies described here,three 100 nt single gRNAs (sgRNAs) targeted to different sequenceswithin EGFP were used, as follows:

(SEQ ID NO: 1) EGFP Site 1 GGGCACGGGCAGCTTGCCGGTGG (SEQ ID NO: 2)EGFP Site 2 GATGCCGTTCTTCTGCTTGTCGG (SEQ ID NO: 3) EGFP Site 3GGTGGTGCAGATGAACTTCAGGGEach of these sgRNAs can efficiently direct Cas9-mediated disruption ofEGFP expression (see Example 1e and 2a, and FIGS. 3E (top) and 3F(top)).

In initial experiments, the effects of single nucleotide mismatches at19 of 20 nucleotides in the complementary targeting region of threeEGFP-targeted sgRNAs were tested. To do this, variant sgRNAs weregenerated for each of the three target sites harboring Watson-Cricktransversion mismatches at positions 1 through 19 (numbered 1 to 20 inthe 3′ to 5′ direction; see FIG. 1) and the abilities of these varioussgRNAs to direct Cas9-mediated EGFP disruption in human cells tested(variant sgRNAs bearing a substitution at position 20 were not generatedbecause this nucleotide is part of the U6 promoter sequence andtherefore must remain a guanine to avoid affecting expression.)

For EGFP target site #2, single mismatches in positions 1-10 of the gRNAhave dramatic effects on associated Cas9 activity (FIG. 2C, middlepanel), consistent with previous studies that suggest mismatches at the5′ end of gRNAs are better tolerated than those at the 3′ end (Jiang etal., Nat Biotechnol 31, 233-239 (2013); Cong et al., Science 339,819-823 (2013); Jinek et al., Science 337, 816-821 (2012)). However,with EGFP target sites #1 and #3, single mismatches at all but a fewpositions in the gRNA appear to be well tolerated, even within the 3′end of the sequence. Furthermore, the specific positions that weresensitive to mismatch differed for these two targets (FIG. 2C, comparetop and bottom panels) for example, target site #1 was particularlysensitive to a mismatch at position 2 whereas target site #3 was mostsensitive to mismatches at positions 1 and 8.

Example 1b. Multiple Mismatches

To test the effects of more than one mismatch at the gRNA/DNA interface,a series of variant sgRNAs bearing double Watson-Crick transversionmismatches in adjacent and separated positions were created and theabilities of these sgRNAs to direct Cas9 nuclease activity were testedin human cells using the EGFP disruption assay. All three target sitesgenerally showed greater sensitivity to double alterations in which oneor both mismatches occur within the 3′ half of the gRNA targetingregion. However, the magnitude of these effects exhibited site-specificvariation, with target site #2 showing the greatest sensitivity to thesedouble mismatches and target site #1 generally showing the least. Totest the number of adjacent mismatches that can be tolerated, variantsgRNAs were constructed bearing increasing numbers of mismatchedpositions ranging from positions 19 to 15 in the 5′ end of the gRNAtargeting region (where single and double mismatches appeared to bebetter tolerated).

Testing of these increasingly mismatched sgRNAs revealed that for allthree target sites, the introduction of three or more adjacentmismatches results in significant loss of RGN activity. A sudden dropoff in activity occurred for three different EGFP-targeted gRNAs as onemakes progressive mismatches starting from position 19 in the 5′ end andadding more mismatches moving toward the 3′ end. Specifically, gRNAscontaining mismatches at positions 19 and 19+18 show essentially fullactivity whereas those with mismatches at positions 19+18+17,19+18+17+16, and 19+18+17+16+15 show essentially no difference relativeto a negative control (FIG. 2F). (Note that we did not mismatch position20 in these variant gRNAs because this position needs to remain as a Gbecause it is part of the U6 promoter that drives expression of thegRNA.)

Additional proof of that shortening gRNA complementarity might lead toRGNs with greater specificities was obtained in the followingexperiment: for four different EGFP-targeted gRNAs (FIG. 2H),introduction of a double mismatch at positions 18 and 19 did notsignificantly impact activity. However, introduction of another doublemismatch at positions 10 and 11 then into these gRNAs results in nearcomplete loss of activity. Interestingly introduction of only the 10/11double mismatches does not generally have as great an impact onactivity.

Taken together, these results in human cells confirm that the activitiesof RGNs can be more sensitive to mismatches in the 3′ half of the gRNAtargeting sequence. However, the data also clearly reveal that thespecificity of RGNs is complex and target site-dependent, with singleand double mismatches often well tolerated even when one or moremismatches occur in the 3′ half of the gRNA targeting region.Furthermore, these data also suggest that not all mismatches in the 5′half of the gRNA/DNA interface are necessarily well tolerated.

In addition, these results strongly suggest that gRNAs bearing shorterregions of complementarity (specifically 17 nts) will be more specificin their activities. We note that 17 nts of specificity combined withthe 2 nts of specificity conferred by the PAM sequence results inspecification of a 19 bp sequence, one of sufficient length to be uniquein large complex genomes such as those found in human cells.

Example 1c. Off-Target Mutations

To determine whether off-target mutations for RGNs targeted toendogenous human genes could be identified, six sgRNAs that target threedifferent sites in the VEGFA gene, one in the EMX1 gene, one in the RNF2gene, and one in the FANCF gene were used. These six sgRNAs efficientlydirected Cas9-mediated indels at their respective endogenous loci inhuman U2OS.EGFP cells as detected by T7 Endonuclease I (T7EI) assay(Methods above). For each of these six RGNs, we then examined dozens ofpotential off-target sites (ranging in number from 46 to as many as 64)for evidence of nuclease-induced NHEJ-mediated indel mutations inU2OS.EGFP cells. The loci assessed included all genomic sites thatdiffer by one or two nucleotides as well as subsets of genomic sitesthat differ by three to six nucleotides and with a bias toward thosethat had one or more of these mismatches in the 5′ half of the gRNAtargeting sequence. Using the T7EI assay, four off-target sites (out of53 candidate sites examined) for VEGFA site 1, twelve (out of 46examined) for VEGFA site 2, seven (out of 64 examined) for VEGFA site 3and one (out of 46 examined) for the EMX1 site were readily identified.No off-target mutations were detected among the 43 and 50 potentialsites examined for the RNF2 or FANCF genes, respectively. The rates ofmutation at verified off-target sites were very high, ranging from 5.6%to 125% (mean of 40%) of the rate observed at the intended target site.These bona fide off-targets included sequences with mismatches in the 3′end of the target site and with as many as a total of five mismatches,with most off-target sites occurring within protein coding genes. DNAsequencing of a subset of off-target sites provided additional molecularconfirmation that indel mutations occur at the expected RGN cleavagesite (FIGS. 8A-C).

Example 1d. Off-Target Mutations in Other Cell Types

Having established that RGNs can induce off-target mutations with highfrequencies in U2OS.EGFP cells, it was next sought to determine whetherthese nucleases would also have these effects in other types of humancells. U2OS.EGFP cells had been chosen for initial experiments becausethese cells were previously used to evaluate the activities of TALENs¹⁵but human HEK293 and K562 cells have been more widely used to test theactivities of targeted nucleases. Therefore, the activities of the fourRGNs targeted to VEGFA sites 1, 2, and 3 and the EMX1 site were alsoassessed in HEK293 and K562 cells. Each of these four RGNs efficientlyinduced NHEJ-mediated indel mutations at their intended on-target sitein these two additional human cell lines (as assessed by T7EI assay),albeit with somewhat lower mutation frequencies than those observed inU2OS.EGFP cells. Assessment of the 24 off-target sites for these fourRGNs originally identified in U2OS.EGFP cells revealed that many wereagain mutated in HEK293 and K562 cells with frequencies similar to thoseat their corresponding on-target site. As expected, DNA sequencing of asubset of these off-target sites from HEK293 cells provided additionalmolecular evidence that alterations are occurring at the expectedgenomic loci. It is not known for certain why in HEK293 cells four andin K562 cells eleven of the off-target sites identified in U2OS.EGFPcells did not show detectable mutations. However, many of theseoff-target sites also showed relatively lower mutation frequencies inU2OS.EGFP cells. Therefore, mutation rates of these sites in HEK293 andK562 cells may be falling below the reliable detection limit of our T7EIassay (-2-5%) because RGNs generally appear to have lower activities inHEK293 and K562 cells compared with U2OS.EGFP cells in our experiments.Taken together, the results in HEK293 and K562 cells provide evidencethat the high-frequency off-target mutations we observe with RGNs willbe a general phenomenon seen in multiple human cell types.

Example 1e. Titration of gRNA- and Cas9-Expressing Plasmid Amounts Usedfor the EGFP Disruption Assay

Single guide RNAs (sgRNAs) were generated for three different sequences(EGFP SITES 1-3, shown above) located upstream of EGFP nucleotide 502, aposition at which the introduction of frameshift mutations vianon-homologous end-joining can robustly disrupt expression of EGFP(Maeder, M. L. et al., Mol Cell 31, 294-301 (2008); Reyon, D. et al.,Nat Biotech 30, 460-465 (2012)).

For each of the three target sites, a range of gRNA-expressing plasmidamounts (12.5 to 250 ng) was initially transfected together with 750 ngof a plasmid expressing a codon-optimized version of the Cas9 nucleaseinto our U2OS.EGFP reporter cells bearing a single copy, constitutivelyexpressed EGFP-PEST reporter gene. All three RGNs efficiently disruptedEGFP expression at the highest concentration of gRNA plasmid (250 ng)(FIG. 3E (top)). However, RGNs for target sites #1 and #3 exhibitedequivalent levels of disruption when lower amounts of gRNA-expressingplasmid were transfected whereas RGN activity at target site #2 droppedimmediately when the amount of gRNA-expressing plasmid transfected wasdecreased (FIG. 3E (top)).

The amount of Cas9-encoding plasmid (range from 50 ng to 750 ng)transfected into our U2OS.EGFP reporter cells was titrated EGFPdisruption assayed. As shown in FIG. 3F (top), target site #1 tolerateda three-fold decrease in the amount of Cas9-encoding plasmid transfectedwithout substantial loss of EGFP disruption activity. However, theactivities of RGNs targeting target sites #2 and #3 decreasedimmediately with a three-fold reduction in the amount of Cas9 plasmidtransfected (FIG. 3F (top)). Based on these results, 25 ng/250 ng, 250ng/750 ng, and 200 ng/750 ng of gRNA-/Cas9-expressing plasmids were usedfor EGFP target sites #1, #2, and #3, respectively, for the experimentsdescribed in Examples 1a-1d.

The reasons why some gRNA/Cas9 combinations work better than others indisrupting EGFP expression is not understood, nor is why some of thesecombinations are more or less sensitive to the amount of plasmids usedfor transfection. Although it is possible that the range of off-targetsites present in the genome for these three sgRNAs might influence eachof their activities, no differences were seen in the numbers of genomicsites that differ by one to six bps for each of these particular targetsites (Table 1) that would account for the differential behavior of thethree sgRNAs.

TABLE 1 Numbers of off-target sites in the human genome for six RGNstargeted to endogenous human genes and three RGNs targeted to the EGFPreporter gene Number of mismatches to on-target site Target Site 0 1 2 34 5 6 Target 1 (VEGFA Site 1) 1 1 4 32 280 2175 13873 Target 2 (VEGFASite 2) 1 0 2 35 443 3889 17398 Target 3 (VEGFA Site 3) 1 1 17 377 602813398 35517 Target 4 (EMX) 1 0 1 18 276 2309 15731 Target 5 (RNF2) 1 0 06 116 976 7443 Target 6 (FANCF) 1 0 1 18 271 1467 9551 EGFP Target Site#1 0 0 3 10 156 1365 9755 EGFP Target Site #2 0 0 0 11 96 974 7353 EGFPTarget Site #3 0 0 1 14 165 1439 10361 Off-target sites for each of thesix RGNs targeted to the VEGFA, RNF2, FANCF, and EMX1 genes and thethree RGNs targeted to EGFP Target Sites #1, #2 and #3 were identifiedin human genome sequence build GRCh37. Mismatches were only allowed forthe 20 nt region to which the gRNA anneals and not to the PAM sequence.

Example 2: Using Pairs of GuideRNAs with FokI-dCas9 Fusion Proteins

Monomeric CRISPR-Cas9 nucleases are widely used for targeted genomeediting but can induce unwanted off-target mutations with highfrequencies. This example describes new dimeric RNA-guided FokINucleases (RFNs) that recognize an extended, double-length sequence andthat strictly depend on two single guide RNAs (gRNAs) for cleavageactivity. RFNs can robustly edit DNA sequences in endogenous human geneswith high efficiencies. Additionally, a method for expressing gRNAsbearing any 5′ end nucleotide is described, a critical advance thatgives dimeric RFNs a useful targeting range. In direct comparisons,monomeric Cas9 nickases generally induce unwanted indels and unexpectedfocal point mutations with higher frequencies than RFNs directed by amatched single gRNA. RFNs combine the ease of CRISPR RNA-based targetingwith the specificity enhancements of dimerization and provide animportant new platform for research and therapeutic applications thatrequire highly precise genome editing.

Materials and Methods

The following materials and methods were used in Example 2.

Single and Multiplex gRNA Expression Plasmids

Plasmids encoding single or multiplex gRNAs were assembled in asingle-step ligation of annealed target site oligosduplexes (IntegratedDNA Technologies) and a constant region oligoduplex (for multiplexgRNAs) with BsmBI-digested Csy4-flanked gRNA backbone (pSQT1313;Addgene).

Multiplex gRNA encoding plasmids were constructed by ligating: 1)annealed oligos encoding the first target site, 2) phosphorylatedannealed oligos encoding crRNA, tracrRNA, and Csy4-binding site, and 3)annealed oligos encoding the second target site, into a U6-Csy4site-gRNAplasmid backbone digested with BsmBI Type IIs restriction enzyme. Csy4RNA binding sites were attached to the 3′ and 5′ ends of a gRNA sequenceand expressed with Cas9 in cells. The Csy4 RNA binding site sequence‘GUUCACUGCCGUAUAGGCAGCUAAGAAA’ (SEQ ID NO:20) was fused to the 5′ and 3′end of the standard gRNA sequence.

(SEQ ID NO: 21) GUUCACUGCCGUAUAGGCAGNNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCGUUCACUGCCGUAUAGGCAGNNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCGUUCACUGCCGUA UAGGCAGThis sequence is a multiplex gRNA sequence flanked by Csy4 sites(underlined). Functionally, encoding these in multiplex on onetranscript should have the same result as encoding them separately.Although all pairs of Csy4-flanked sgRNAs were expressed in a multiplexcontext in the experiments described herein, the sgRNAs can be encodedin multiplex sgRNAs separated by Csy4 sites encoded on one transcript aswell as individual sgRNAs that have an additional Csy4 sequence. In thissequence, the first N20 sequence represents the sequence complementaryto one strand of the target genomic sequence, and the second N20sequence represents the sequence complementary to the other strand ofthe target genomic sequence.

A plasmid encoding the Csy4 recognition site containing gRNA wasco-transfected with plasmid encoding Cas9 and Csy4 proteins separated bya ‘2A’ peptide linkage. The results showed that gRNAs with Csy4 sitesfused to the 5′ and 3′ ends remained capable of directing Cas9-mediatedcleavage in human cells using the U2OS-EGFP disruption assay previouslydescribed. Thus, Csy4 RNA binding sites can be attached to 3′ end of agRNA sequence and complexes of these Csy4 site-containing gRNAs withCas9 remain functional in the cell.

In some experiments, a construct encoding Csy4-T2A-FokI-dCas9 was used.The sequences of the FokI-dCas9 fusions are shown below, and include aGGGGS (SEQ ID NO:23) linker (underlined) between the FokI and dCas9 anda nuclear localization sequence.

FokI-dCas9 amino acid sequence (FokI-G4S-dCas9-nls-3XFLAG)(SEQ ID NO: 24) MQLVKSELEEKKSELRHKLKYVPHEYIELIEIARNSTQDRILEMKVMEFFMKVYGYRGKHLGGSRKPDGAIYTVGSPIDYGVIVDTKAYSGGYNLPIGQADEMQRYVEENQTRNKHINPNEWWKVYPSSVTEFKFLFVSGHFKGNYKAQLTRLNHITNCNGAVLSVEELLIGGEMIKAGTLTLEEVRRKFNNGEINFGGGGSDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKINRKVIVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDAIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGDGSPKKKRKVSSDYKDHDGDYKDHDIDYKDDD DK FokI-dCas9 nucleotide sequence (FokI-G4S-dCas9-nls-3XFLAG)(SEQ ID NO: 25) ATGCAACTAGTCAAAAGTGAACTGGAGGAGAAGAAATCTGAACTTCGTCATAAATTGAAATATGTGCCTCATGAATATATTGAATTAATTGAAATTGCCAGAAATTCCACTCAGGATAGAATTCTTGAAATGAAGGTAATGGAATTTTTTATGAAAGTTTATGGATATAGAGGTAAACATTTGGGTGGATCAAGGAAACCGGACGGAGCAATTTATACTGTCGGATCTCCTATTGATTACGGTGTGATCGTGGATACTAAAGCTTATAGCGGAGGTTATAATCTGCCAATTGGCCAAGCAGATGAAATGCAACGATATGTCGAAGAAAATCAAACACGAAACAAACATATCAACCCTAATGAATGGTGGAAAGTCTATCCATCTTCTGTAACGGAATTTAAGTTTTTATTTGTGAGTGGTCACTTTAAAGGAAACTACAAAGCTCAGCTTACACGATTAAATCATATCACTAATTGTAATGGAGCTGTTCTTAGTGTAGAAGAGCTTTTAATTGGTGGAGAAATGATTAAAGCCGGCACATTAACCTTAGAGGAAGTCAGACGGAAATTTAATAACGGCGAGATAAACTTTGGTGGCGGTGGATCCGATAAAAAGTATTCTATTGGTTTAGCCATCGGCACTAATTCCGTTGGATGGGCTGTCATAACCGATGAATACAAAGTACCTTCAAAGAAATTTAAGGTGTTGGGGAACACAGACCGTCATTCGATTAAAAAGAATCTTATCGGTGCCCTCCTATTCGATAGTGGCGAAACGGCAGAGGCGACTCGCCTGAAACGAACCGCTCGGAGAAGGTATACACGTCGCAAGAACCGAATATGTTACTTACAAGAAATTTTTAGCAATGAGATGGCCAAAGTTGACGATTCTTTCTTTCACCGTTTGGAAGAGTCCTTCCTTGTCGAAGAGGACAAGAAACATGAACGGCACCCCATCTTTGGAAACATAGTAGATGAGGTGGCATATCATGAAAAGTACCCAACGATTTATCACCTCAGAAAAAAGCTAGTTGACTCAACTGATAAAGCGGACCTGAGGTTAATCTACTTGGCTCTTGCCCATATGATAAAGTTCCGTGGGCACTTTCTCATTGAGGGTGATCTAAATCCGGACAACTCGGATGTCGACAAACTGTTCATCCAGTTAGTACAAACCTATAATCAGTTGTTTGAAGAGAACCCTATAAATGCAAGTGGCGTGGATGCGAAGGCTATTCTTAGCGCCCGCCTCTCTAAATCCCGACGGCTAGAAAACCTGATCGCACAATTACCCGGAGAGAAGAAAAATGGGTTGTTCGGTAACCTTATAGCGCTCTCACTAGGCCTGACACCAAATTTTAAGTCGAACTTCGACTTAGCTGAAGATGCCAAATTGCAGCTTAGTAAGGACACGTACGATGACGATCTCGACAATCTACTGGCACAAATTGGAGATCAGTATGCGGACTTATTTTTGGCTGCCAAAAACCTTAGCGATGCAATCCTCCTATCTGACATACTGAGAGTTAATACTGAGATTACCAAGGCGCCGTTATCCGCTTCAATGATCAAAAGGTACGATGAACATCACCAAGACTTGACACTTCTCAAGGCCCTAGTCCGTCAGCAACTGCCTGAGAAATATAAGGAAATATTCTTTGATCAGTCGAAAAACGGGTACGCAGGTTATATTGACGGCGGAGCGAGTCAAGAGGAATTCTACAAGTTTATCAAACCCATATTAGAGAAGATGGATGGGACGGAAGAGTTGCTTGTAAAACTCAATCGCGAAGATCTACTGCGAAAGCAGCGGACTTTCGACAACGGTAGCATTCCACATCAAATCCACTTAGGCGAATTGCATGCTATACTTAGAAGGCAGGAGGATTTTTATCCGTTCCTCAAAGACAATCGTGAAAAGATTGAGAAAATCCTAACCTTTCGCATACCTTACTATGTGGGACCCCTGGCCCGAGGGAACTCTCGGTTCGCATGGATGACAAGAAAGTCCGAAGAAACGATTACTCCATGGAATTTTGAGGAAGTTGTCGATAAAGGTGCGTCAGCTCAATCGTTCATCGAGAGGATGACCAACTTTGACAAGAATTTACCGAACGAAAAAGTATTGCCTAAGCACAGTTTACTTTACGAGTATTTCACAGTGTACAATGAACTCACGAAAGTTAAGTATGTCACTGAGGGCATGCGTAAACCCGCCTTTCTAAGCGGAGAACAGAAGAAAGCAATAGTAGATCTGTTATTCAAGACCAACCGCAAAGTGACAGTTAAGCAATTGAAAGAGGACTACTTTAAGAAAATTGAATGCTTCGATTCTGTCGAGATCTCCGGGGTAGAAGATCGATTTAATGCGTCACTTGGTACGTATCATGACCTCCTAAAGATAATTAAAGATAAGGACTTCCTGGATAACGAAGAGAATGAAGATATCTTAGAAGATATAGTGTTGACTCTTACCCTCTTTGAAGATCGGGAAATGATTGAGGAAAGACTAAAAACATACGCTCACCTGTTCGACGATAAGGTTATGAAACAGTTAAAGAGGCGTCGCTATACGGGCTGGGGACGATTGTCGCGGAAACTTATCAACGGGATAAGAGACAAGCAAAGTGGTAAAACTATTCTCGATTTTCTAAAGAGCGACGGCTTCGCCAATAGGAACTTTATGCAGCTGATCCATGATGACTCTTTAACCTTCAAAGAGGATATACAAAAGGCACAGGTTTCCGGACAAGGGGACTCATTGCACGAACATATTGCGAATCTTGCTGGTTCGCCAGCCATCAAAAAGGGCATACTCCAGACAGTCAAAGTAGTGGATGAGCTAGTTAAGGTCATGGGACGTCACAAACCGGAAAACATTGTAATCGAGATGGCACGCGAAAATCAAACGACTCAGAAGGGGCAAAAAAACAGTCGAGAGCGGATGAAGAGAATAGAAGAGGGTATTAAAGAACTGGGCAGCCAGATCTTAAAGGAGCATCCTGTGGAAAATACCCAATTGCAGAACGAGAAACTTTACCTCTATTACCTACAAAATGGAAGGGACATGTATGTTGATCAGGAACTGGACATAAACCGTTTATCTGATTACGACGTCGATGCCATTGTACCCCAATCCTTTTTGAAGGACGATTCAATCGACAATAAAGTGCTTACACGCTCGGATAAGAACCGAGGGAAAAGTGACAATGTTCCAAGCGAGGAAGTCGTAAAGAAAATGAAGAACTATTGGCGGCAGCTCCTAAATGCGAAACTGATAACGCAAAGAAAGTTCGATAACTTAACTAAAGCTGAGAGGGGTGGCTTGTCTGAACTTGACAAGGCCGGATTTATTAAACGTCAGCTCGTGGAAACCCGCCAAATCACAAAGCATGTTGCACAGATACTAGATTCCCGAATGAATACGAAATACGACGAGAACGATAAGCTGATTCGGGAAGTCAAAGTAATCACTTTAAAGTCAAAATTGGTGTCGGACTTCAGAAAGGATTTTCAATTCTATAAAGTTAGGGAGATAAATAACTACCACCATGCGCACGACGCTTATCTTAATGCCGTCGTAGGGACCGCACTCATTAAGAAATACCCGAAGCTAGAAAGTGAGTTTGTGTATGGTGATTACAAAGTTTATGACGTCCGTAAGATGATCGCGAAAAGCGAACAGGAGATAGGCAAGGCTACAGCCAAATACTTCTTTTATTCTAACATTATGAATTTCTTTAAGACGGAAATCACTCTGGCAAACGGAGAGATACGCAAACGACCTTTAATTGAAACCAATGGGGAGACAGGTGAAATCGTATGGGATAAGGGCCGGGACTTCGCGACGGTGAGAAAAGTTTTGTCCATGCCCCAAGTCAACATAGTAAAGAAAACTGAGGTGCAGACCGGAGGGTTTTCAAAGGAATCGATTCTTCCAAAAAGGAATAGTGATAAGCTCATCGCTCGTAAAAAGGACTGGGACCCGAAAAAGTACGGTGGCTTCGATAGCCCTACAGTTGCCTATTCTGTCCTAGTAGTGGCAAAAGTTGAGAAGGGAAAATCCAAGAAACTGAAGTCAGTCAAAGAATTATTGGGGATAACGATTATGGAGCGCTCGTCTTTTGAAAAGAACCCCATCGACTTCCTTGAGGCGAAAGGTTACAAGGAAGTAAAAAAGGATCTCATAATTAAACTACCAAAGTATAGTCTGTTTGAGTTAGAAAATGGCCGAAAACGGATGTTGGCTAGCGCCGGAGAGCTTCAAAAGGGGAACGAACTCGCACTACCGTCTAAATACGTGAATTTCCTGTATTTAGCGTCCCATTACGAGAAGTTGAAAGGTTCACCTGAAGATAACGAACAGAAGCAACTTTTTGTTGAGCAGCACAAACATTATCTCGACGAAATCATAGAGCAAATTTCGGAATTCAGTAAGAGAGTCATCCTAGCTGATGCCAATCTGGACAAAGTATTAAGCGCATACAACAAGCACAGGGATAAACCCATACGTGAGCAGGCGGAAAATATTATCCATTTGTTTACTCTTACCAACCTCGGCGCTCCAGCCGCATTCAAGTATTTTGACACAACGATAGATCGCAAACGATACACTTCTACCAAGGAGGTGCTAGACGCGACACTGATTCACCAATCCATCACGGGATTATATGAAACTCGGATAGATTTGTCACAGCTTGGGGGTGACGGATCCCCCAAGAAGAAGAGGAAAGTCTCGAGCGACTACAAAGACCATGACGGTGATTATAAAGATCATGACATCGATTACAAGGATGACGAT GACAAGTGA

Alternatively, a human codon optimized version of the construct wasused, which contained both N- and C-terminal nuclear localizationsignals, as shown below.

Nls-FokI-dCas9-nls amino acid sequence (SEQ ID NO: 26)MPKKKRKVSSQLVKSELEEKKSELRHKLKYVPHEYIELIEIARNSTQDRILEMKVMEFFMKVYGYRGKHLGGSRKPDGAIYTVGSPIDYGVIVDTKAYSGGYNLPIGQADEMQRYVEENQTRNKHINPNEWWKVYPSSVTEFKFLFVSGHFKGNYKAQLTRLNHITNCNGAVLSVEELLIGGEMIKAGTLTLEEVRRKFNNGEINFGGGGSDKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLILLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDAIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGDGSPKKKRKVSSDYKDHDGDYKD HDIDYKDDDDKNls-FokI-dCas9-nls nucleotide sequence (SEQ ID NO: 27)ATGCCTAAGAAGAAGCGGAAGGTGAGCAGCCAACTTGTGAAGTCTGAACTCGAGGAGAAAAAATCAGAGTTGAGACACAAGTTGAAGTACGTGCCACACGAATACATCGAGCTTATCGAGATCGCCAGAAACAGTACCCAGGATAGGATCCTTGAGATGAAAGTCATGGAGTTCTTTATGAAGGTCTACGGTTATAGAGGAAAGCACCTTGGCGGTAGCAGAAAGCCCGATGGCGCCATCTATACTGTCGGATCTCCTATCGATTATGGGGTGATCGTGGATACCAAAGCTTACTCAGGCGGGTACAACTTGCCCATAGGACAAGCCGACGAGATGCAGCGGTATGTCGAAGAGAACCAGACGCGCAACAAGCACATCAACCCCAATGAATGGTGGAAAGTGTACCCAAGTAGTGTGACTGAGTTCAAGTTCCTGTTTGTCTCCGGCCACTTTAAGGGCAATTATAAAGCTCAGCTCACTAGACTCAATCACATCACAAACTGCAACGGAGCTGTGTTGTCAGTGGAGGAGCTCCTGATTGGAGGCGAGATGATCAAAGCCGGCACCCTTACACTGGAGGAGGTGCGGCGGAAGTTCAACAATGGAGAGATCAACTTCGGTGGCGGTGGATCCGATAAAAAGTATTCTATTGGTTTAGCCATCGGCACTAATTCCGTTGGATGGGCTGTCATAACCGATGAATACAAAGTACCTTCAAAGAAATTTAAGGTGTTGGGGAACACAGACCGTCATTCGATTAAAAAGAATCTTATCGGTGCCCTCCTATTCGATAGTGGCGAAACGGCAGAGGCGACTCGCCTGAAACGAACCGCTCGGAGAAGGTATACACGTCGCAAGAACCGAATATGTTACTTACAAGAAATTTTTAGCAATGAGATGGCCAAAGTTGACGATTCTTTCTTTCACCGTTTGGAAGAGTCCTTCCTTGTCGAAGAGGACAAGAAACATGAACGGCACCCCATCTTTGGAAACATAGTAGATGAGGTGGCATATCATGAAAAGTACCCAACGATTTATCACCTCAGAAAAAAGCTAGTTGACTCAACTGATAAAGCGGACCTGAGGTTAATCTACTTGGCTCTTGCCCATATGATAAAGTTCCGTGGGCACTTTCTCATTGAGGGTGATCTAAATCCGGACAACTCGGATGTCGACAAACTGTTCATCCAGTTAGTACAAACCTATAATCAGTTGTTTGAAGAGAACCCTATAAATGCAAGTGGCGTGGATGCGAAGGCTATTCTTAGCGCCCGCCTCTCTAAATCCCGACGGCTAGAAAACCTGATCGCACAATTACCCGGAGAGAAGAAAAATGGGTTGTTCGGTAACCTTATAGCGCTCTCACTAGGCCTGACACCAAATTTTAAGTCGAACTTCGACTTAGCTGAAGATGCCAAATTGCAGCTTAGTAAGGACACGTACGATGACGATCTCGACAATCTACTGGCACAAATTGGAGATCAGTATGCGGACTTATTTTTGGCTGCCAAAAACCTTAGCGATGCAATCCTCCTATCTGACATACTGAGAGTTAATACTGAGATTACCAAGGCGCCGTTATCCGCTTCAATGATCAAAAGGTACGATGAACATCACCAAGACTTGACACTTCTCAAGGCCCTAGTCCGTCAGCAACTGCCTGAGAAATATAAGGAAATATTCTTTGATCAGTCGAAAAACGGGTACGCAGGTTATATTGACGGCGGAGCGAGTCAAGAGGAATTCTACAAGTTTATCAAACCCATATTAGAGAAGATGGATGGGACGGAAGAGTTGCTTGTAAAACTCAATCGCGAAGATCTACTGCGAAAGCAGCGGACTTTCGACAACGGTAGCATTCCACATCAAATCCACTTAGGCGAATTGCATGCTATACTTAGAAGGCAGGAGGATTTTTATCCGTTCCTCAAAGACAATCGTGAAAAGATTGAGAAAATCCTAACCTTTCGCATACCTTACTATGTGGGACCCCTGGCCCGAGGGAACTCTCGGTTCGCATGGATGACAAGAAAGTCCGAAGAAACGATTACTCCATGGAATTTTGAGGAAGTTGTCGATAAAGGTGCGTCAGCTCAATCGTTCATCGAGAGGATGACCAACTTTGACAAGAATTTACCGAACGAAAAAGTATTGCCTAAGCACAGTTTACTTTACGAGTATTTCACAGTGTACAATGAACTCACGAAAGTTAAGTATGTCACTGAGGGCATGCGTAAACCCGCCTTTCTAAGCGGAGAACAGAAGAAAGCAATAGTAGATCTGTTATTCAAGACCAACCGCAAAGTGACAGTTAAGCAATTGAAAGAGGACTACTTTAAGAAAATTGAATGCTTCGATTCTGTCGAGATCTCCGGGGTAGAAGATCGATTTAATGCGTCACTTGGTACGTATCATGACCTCCTAAAGATAATTAAAGATAAGGACTTCCTGGATAACGAAGAGAATGAAGATATCTTAGAAGATATAGTGTTGACTCTTACCCTCTTTGAAGATCGGGAAATGATTGAGGAAAGACTAAAAACATACGCTCACCTGTTCGACGATAAGGTTATGAAACAGTTAAAGAGGCGTCGCTATACGGGCTGGGGACGATTGTCGCGGAAACTTATCAACGGGATAAGAGACAAGCAAAGTGGTAAAACTATTCTCGATTTTCTAAAGAGCGACGGCTTCGCCAATAGGAACTTTATGCAGCTGATCCATGATGACTCTTTAACCTTCAAAGAGGATATACAAAAGGCACAGGTTTCCGGACAAGGGGACTCATTGCACGAACATATTGCGAATCTTGCTGGTTCGCCAGCCATCAAAAAGGGCATACTCCAGACAGTCAAAGTAGTGGATGAGCTAGTTAAGGTCATGGGACGTCACAAACCGGAAAACATTGTAATCGAGATGGCACGCGAAAATCAAACGACTCAGAAGGGGCAAAAAAACAGTCGAGAGCGGATGAAGAGAATAGAAGAGGGTATTAAAGAACTGGGCAGCCAGATCTTAAAGGAGCATCCTGTGGAAAATACCCAATTGCAGAACGAGAAACTTTACCTCTATTACCTACAAAATGGAAGGGACATGTATGTTGATCAGGAACTGGACATAAACCGTTTATCTGATTACGACGTCGATGCCATTGTACCCCAATCCTTTTTGAAGGACGATTCAATCGACAATAAAGTGCTTACACGCTCGGATAAGAACCGAGGGAAAAGTGACAATGTTCCAAGCGAGGAAGTCGTAAAGAAAATGAAGAACTATTGGCGGCAGCTCCTAAATGCGAAACTGATAACGCAAAGAAAGTTCGATAACTTAACTAAAGCTGAGAGGGGTGGCTTGTCTGAACTTGACAAGGCCGGATTTATTAAACGTCAGCTCGTGGAAACCCGCCAAATCACAAAGCATGTTGCACAGATACTAGATTCCCGAATGAATACGAAATACGACGAGAACGATAAGCTGATTCGGGAAGTCAAAGTAATCACTTTAAAGTCAAAATTGGTGTCGGACTTCAGAAAGGATTTTCAATTCTATAAAGTTAGGGAGATAAATAACTACCACCATGCGCACGACGCTTATCTTAATGCCGTCGTAGGGACCGCACTCATTAAGAAATACCCGAAGCTAGAAAGTGAGTTTGTGTATGGTGATTACAAAGTTTATGACGTCCGTAAGATGATCGCGAAAAGCGAACAGGAGATAGGCAAGGCTACAGCCAAATACTTCTTTTATTCTAACATTATGAATTTCTTTAAGACGGAAATCACTCTGGCAAACGGAGAGATACGCAAACGACCTTTAATTGAAACCAATGGGGAGACAGGTGAAATCGTATGGGATAAGGGCCGGGACTTCGCGACGGTGAGAAAAGTTTTGTCCATGCCCCAAGTCAACATAGTAAAGAAAACTGAGGTGCAGACCGGAGGGTTTTCAAAGGAATCGATTCTTCCAAAAAGGAATAGTGATAAGCTCATCGCTCGTAAAAAGGACTGGGACCCGAAAAAGTACGGTGGCTTCGATAGCCCTACAGTTGCCTATTCTGTCCTAGTAGTGGCAAAAGTTGAGAAGGGAAAATCCAAGAAACTGAAGTCAGTCAAAGAATTATTGGGGATAACGATTATGGAGCGCTCGTCTTTTGAAAAGAACCCCATCGACTTCCTTGAGGCGAAAGGTTACAAGGAAGTAAAAAAGGATCTCATAATTAAACTACCAAAGTATAGTCTGTTTGAGTTAGAAAATGGCCGAAAACGGATGTTGGCTAGCGCCGGAGAGCTTCAAAAGGGGAACGAACTCGCACTACCGTCTAAATACGTGAATTTCCTGTATTTAGCGTCCCATTACGAGAAGTTGAAAGGTTCACCTGAAGATAACGAACAGAAGCAACTTTTTGTTGAGCAGCACAAACATTATCTCGACGAAATCATAGAGCAAATTTCGGAATTCAGTAAGAGAGTCATCCTAGCTGATGCCAATCTGGACAAAGTATTAAGCGCATACAACAAGCACAGGGATAAACCCATACGTGAGCAGGCGGAAAATATTATCCATTTGTTTACTCTTACCAACCTCGGCGCTCCAGCCGCATTCAAGTATTTTGACACAACGATAGATCGCAAACGATACACTTCTACCAAGGAGGTGCTAGACGCGACACTGATTCACCAATCCATCACGGGATTATATGAAACTCGGATAGATTTGTCACAGCTTGGGGGTGACGGATCCCCCAAGAAGAAGAGGAAAGTCTCGAGCGACTACAAAGACCATGACGGTGATTATAAAGATCATGACATCGATTACAAGGATGACGATGACAAGTGA

Tissue Culture and Transfections

All cell culture experiments were carried out in HEK 293 cells, U2OScells, or in U2OS cells harboring a stably integrated, single-copy,destabilized EGFP gene (U2OS.EGFP cells). Cell lines were cultured inAdvanced DMEM (Life Technologies) supplemented with 10% FBS, 2 mMGlutaMax (Life Technologies) and penicillin/streptomycin at 37C with 5%CO2. Additionally, U2OS.EGFP cells were cultured in the presence of 400μg/ml of G418.

U2OS cells and U2OS.EGFP cells were transfected using the DN-100 programof a Lonza 4D-Nucleofector according to the manufacturer's instructions.In initial FokI-dCas9 activity screens and focused spacer lengthanalysis experiments, 750 ng of pCAG-Csy4-FokI-dCas9-nls nucleaseplasmid and 250 ng of gRNA encoding plasmids were transfected togetherwith 50 ng tdTomato expression plasmid (Clontech) as a transfectioncontrol. In all other experiments in U2OS and U2OS.EGFP cells, 975 ng ofhuman codon optimized pCAG-Csy4-T2A-nls-hFokI-dCas9-nls (SQT1601) orpCAG-Cas9-D10A nickase (NW3) were transfected along with 325 ng of gRNAvector and 10 ng of Td tomato expression plasmid and analyzed 3 daysafter transfection. HEK293 cells were transfected with 750 ng ofnuclease plasmid, 250 ng of gRNA expression plasmid and 10 ng of Tdtomato, using Lipofectamine (Life Technologies) according to themanufacturer's instructions and analyzed for NHEJ-mediated mutagenesis 3days after transfection.

Single transfections were performed for the initial spacer activityscreen, and duplicate transfections for the focused spacer lengthanalysis. All other transfections were performed in triplicate.

EGFP Disruption Assay

The EGFP disruption assay was performed as previously described (seeExample 1 and Reyon et al., Nat Biotech 30, 460-465 (2012)) usingU2OS.EGFP reporter cells. Cells were assayed for EGFP and tdTomatoexpression using an BD Biosciences LSR II or Fortessa FACS analyzer.

Quantification of Nuclease- or Nickase-Induced Mutation Rates by T7EIAssay

T7E1 assays were performed as previously described (Reyon et al., NatBiotech 30, 460-465 (2012)). Briefly, genomic DNA was isolated 72 hourspost transfection using the Agencourt DNAdvance Genomic DNA Isolationkit (Beckman Coulter Genomics) according to the manufacturer'sinstructions with a Sciclone G3 liquid-handling workstation (Caliper).PCR reactions to amplify genomic loci were performed using PhusionHot-start Flex DNA polymerase (New England Biolabs). Samples wereamplified using a two-step protocol (98° C., 30 sec; (98° C., 7 sec; 72°C., 30 sec)×35; 72° C., 5 min) or a touchdown PCR protocol ((98° C., 10s; 72-62° C., −1° C./cycle, 15 s; 72° C., 30 s)×10 cycles, (98° C., 10s; 62° C., 15 s; 72° C., 30 s)×25 cycles). 200 ng of purified PCRamplicons were denatured, hybridized, and treated with T7 Endonuclease I(New England Biolabs). Mutation frequency was quantified using a Qiaxcelcapillary electrophoresis instrument (Qiagen) as previously described(Reyon et al., Nat Biotech 30, 460-465 (2012)).

Sanger Sequencing of Mutagenized Genomic DNA

The same purified PCR products used for T7EI assay were Topo-cloned(Life Technologies) and plasmid DNA of individual clones was isolatedand sequenced using an M13 reverse primer (5′-GTAAAACGACGGCCAG-3; SEQ IDNO:19).

Illumina Library Preparation and Analysis

Short 200-350 bp PCR products were amplified using Phusion Hot-startFLEX DNA polymerase. PCR products were purified using Ampure XP beads(Beckman Coulter Genomics) according to manufacturer's instructions.Dual-indexed TruSeq Illumina deep sequencing libraries were preparedusing a high-throughput library preparation system (Kapa Biosystems) ona Sciclone G3 liquid-handling workstation. Final adapter-ligatedlibraries were quantified using a Qiaxcel capillary electrophoresisinstrument (Qiagen). 150 bp paired end sequencing was performed on anIllumina MiSeq Sequencer by the Dana-Farber Cancer Institute MolecularBiology Core.

MiSeq paired-end reads were mapped to human genome reference GChr37using bwa. Reads with an average quality score >30 were analyzed forinsertion or deletion mutations that overlapped the intended target orcandidate off-target nuclease binding site. Mutation analyses wereconducted using the Genome Analysis Toolkit (GATK) and Python.

Off-Target Search Algorithm:

A target-site matching algorithm was implemented that looks for matcheswith less than a specified number of mismatches in a sliding windowacross the human genome.

Example 2a. Rationale for Designing Dimeric RNA-Guided Nucleases

It was hypothesized that a single platform combining the specificityadvantages of dimerization with the ease of Cas9 targeting could bedeveloped. To do this, the well-characterized, dimerization-dependentFokI nuclease domain was fused to a RNA-guided catalytically inactiveCas9 (dCas9) protein. It was hoped that, like FokI-containing ZFNs andTALENs, dimers of these fusions might mediate sequence-specific DNAcleavage when bound to target sites composed of two “half-sites” with acertain length “spacer” sequence between them (FIG. 4A). Such fusionswere hypothesized to have enhanced specificity because they shouldrequire two gRNAs for activity (FIG. 4A) and because a single gRNA wouldpresumably be too inefficient or unable to recruit the twoFokI-containing fusion proteins required for DNA cleavage. It washypothesized that such a dimeric system would show improved specificityrelative to standard monomeric Cas9 nucleases and also would potentiallypossess important specificity advantages over the paired nickase systemin which single nickases can still exert unwanted mutagenic effects.

Example 2b. Multiplex Expression of gRNAs Without 5′-End NucleotideLimitations

The targeting range for a dimeric RNA-guided nuclease would be low usingexisting gRNA expression methods. Two sequence requirements typicallyrestrict the targeting range of a dCas9 monomer: the requirement for aPAM sequence of 5′-NGG that is specified by the dCas9 and a requirementfor a G nucleotide at the 5′ end of the gRNA imposed by the use of a U6promoter in most expression vectors. If, however, the requirement forthe 5′ G in the gRNA could be relieved, then the targeting range wouldimprove by 16-fold.

To develop a multiplex system that would allow for the expression ofgRNAs with any 5′ nucleotide, a plasmid was constructed from which twogRNAs, each flanked by cleavage sites for the Csy4 ribonuclease(Haurwitz et al., Science 329, 1355-1358 (2010)), can be expressedwithin a single RNA transcribed from a U6 promoter (FIG. 4B). Csy4 wouldbe expected to process this transcript thereby releasing the two gRNAs.Based on the known mechanism of Csy4-mediated cleavage ((Haurwitz etal., Science 329, 1355-1358 (2010); Sternberg et al., RNA 18, 661-672(2012)), each processed gRNA should retain a Csy4 recognition site onits 3′ end with a Csy4 protein bound to that site (FIG. 4B). In thisconfiguration, it should be possible to express gRNAs with any 5′nucleotide. This system was tested by using it to express two gRNAstargeted to sites within the EGFP reporter gene. Co-expression of thistranscript together with Csy4 and Cas9 nucleases in human cells led tothe introduction of indel mutations at both EGFP target sites as well asof deletion of the sequence between these sites (FIG. 4C). Theseexperiments suggest that both gRNAs are being processed from the singleparental RNA transcript and both are capable of directing Cas9 nucleaseactivities in human cells.

Example 2c. Construction and Optimization of Dimeric RNA-GuidedNucleases

Two different hybrid proteins harboring the FokI nuclease domain and thedCas9 protein were constructed: one in which the FokI nuclease domain isfused to the carboxy-terminus of dCas9 (dCas9-FokI) and the other inwhich it is fused to the amino-terminus (FokI-dCas9) (FIG. 5A). ThedCas9-FokI protein is analogous in architecture to ZFNs and TALENs (FIG.5A). To ascertain whether either or both of these fusions could mediatesite-specific cleavage of DNA, a well-established human cell-based assaythat can rapidly and easily quantify the introduction of NHEJ-mediatedindels into an EGFP reporter gene was used (the EGFP disruption assaydescribed above in Example 1). Because the geometry of the half-sitesrequired for efficient cleavage was not known, 60 pairs of gRNAstargeted to various sites in EGFP were designed. The two half-sitestargeted by each of these gRNA pairs were oriented such that both oftheir PAM sequences are either directly adjacent to the spacer sequence(the “PAM in” orientation) or positioned at the outer boundaries of thefull-length target site (the “PAM out” orientation) (FIG. 5B). Inaddition, the spacer sequence was also varied in length from 0 to 31 bps(FIG. 5B and Table 2).

TABLE 2 FokI- dCas9 Target Edge-to- EGFP Start SEQ SEQ edge PairPosition ID ID ‘spacer’ # Name (+) Sequence (+) sites NO:Sequence (−) sites NO: distance PAM  1 EGFP site  74GAGCTGGACGGCGACGTAAACGG  28. CGCCGGACACGCTGAACTTGTGG  29.  0 in 1  2EGFP site 174 CCGGCAAGCTGCCCGTGCCCTGG  30. GGTCAGGGTGGTCACGAGGGTGG  31. 1 in 2  3 EGFP site  37 CGAGGAGCTGTTCACCGGGGTGG  32.CCGTCCAGCTCGACCAGGATGGG  33.  2 in 3  4 EGFP site  37CGAGGAGCTGTTCACCGGGGTGG  34. GCCGTCCAGCTCGACCAGGATGG  35.  3 in 4  5EGFP site 174 CCGGCAAGCTGCCCGTGCCCTGG  36. GTAGGTCAGGGTGGTCACGAGGG  37. 4 in 5  6 EGFP site  34 GGGCGAGGAGCTGTTCACCGGGG  38.CCGTCCAGCTCGACCAGGATGGG  39.  5 in 6  7 EGFP site  33AGGGCGAGGAGCTGTTCACCGGG  40. CCGTCCAGCTCGACCAGGATGGG  41.  6 in 7  8EGFP site  32 AAGGGCGAGGAGCTGTTCACCGG  42. CCGTCCAGCTCGACCAGGATGGG  43. 7 in 8  9 EGFP site  32 AAGGGCGAGGAGCTGTTCACCGG  44.GCCGTCCAGCTCGACCAGGATGG  45.  8 in 9 10 EGFP site 106CAGCGTGTCCGGCGAGGGCGAGG  46. CTTCAGGGTCAGCTTGCCGTAGG  47.  9 in 10 11EGFP site  34 GGGCGAGGAGCTGTTCACCGGGG  48. CGTCGCCGTCCAGCTCGACCAGG  49.10 in 11 12 EGFP site  33 AGGGCGAGGAGCTGTTCACCGGG  50.CGTCGCCGTCCAGCTCGACCAGG  51. 11 in 12 13 EGFP site  32AAGGGCGAGGAGCTGTTCACCGG  52. CGTCGCCGTCCAGCTCGACCAGG  53. 12 in 13 14EGFP site 155 CTGAAGTTCATCTGCACCACCGG  54. GTGGTCACGAGGGTGGGCCAGGG  55.13 in 14 15 EGFP site 101 AAGTTCAGCGTGTCCGGCGAGGG  56.CTTCAGGGTCAGCTTGCCGTAGG  57. 14 in 15 16 EGFP site 100CAAGTTCAGCGTGTCCGGCGAGG  58. CTTCAGGGTCAGCTTGCCGTAGG  59. 15 in 16 17EGFP site  58 GGTGCCCATCCTGGTCGAGCTGG  60. CGCCGGACACGCTGAACTTGTGG  61.16 in 17 18 EGFP site  74 GAGCTGGACGGCGACGTAAACGG  62.GGCATCGCCCTCGCCCTCGCCGG  63. 17 in 18 19 EGFP site 307GGAGCGCACCATCTTCTTCAAGG  64. CTCGAACTTCACCTCGGCGCGGG  65. 18 in 19 20EGFP site 155 CTGAAGTTCATCTGCACCACCGG  66. GTCAGGGTGGTCACGAGGGTGGG  67.19 in 20 21 EGFP site  95 GGCCACAAGTTCAGCGTGTCCGG  68.CTTCAGGGTCAGCTTGCCGTAGG  69. 20 in 21 22 EGFP site 203CTCGTGACCACCCTGACCTACGG  70. CGTGCTGCTTCATGTGGTCGGGG  71. 21 in 22 23EGFP site 174 CCGGCAAGCTGCCCGTGCCCTGG  72. GCTGAAGCACTGCACGCCGTAGG  73.22 in 23 24 EGFP site 107 AGCGTGTCCGGCGAGGGCGAGGG  74.GGTGGTGCAGATGAACTTCAGGG  75. 23 in 24 25 EGFP site 106CAGCGTGTCCGGCGAGGGCGAGG  76. GGTGGTGCAGATGAACTTCAGGG  77. 24 in 25 26EGFP site  49 CACCGGGGTGGTGCCCATCCTGG  78. CGCCGGACACGCTGAACTTGTGG  79.25 in 26 27 EGFP site 122 GGCGAGGGCGATGCCACCTACGG  80.GGGCACGGGCAGCTTGCCGGTGG  81. 26 in 27 28 EGFP site 203CTCGTGACCACCCTGACCTACGG  82. AGAAGTCGTGCTGCTTCATGTGG  83. 27 in 28 29EGFP site 337 CAACTACAAGACCCGCGCCGAGG  84. CGATGCCCTTCAGCTCGATGCGG  85.28 in 29 30 EGFP site  62 CCCATCCTGGTCGAGCTGGACGG  86.GGCATCGCCCTCGCCCTCGCCGG  87. 29 in 30 31 EGFP site 100CAAGTTCAGCGTGTCCGGCGAGG  88. GGTGGTGCAGATGAACTTCAGGG  89. 30 in 31 32EGFP site  74 GAGCTGGACGGCGACGTAAACGG  90. GACCAGGATGGGCACCACCCCGG  91. 0 out 32 33 EGFP site 314 ACCATCTTCTTCAAGGACGACGG  92.CGCTCCTGGACGTAGCCTTCGGG  93.  1 out 33 34 EGFP site 122GGCGAGGGCGATGCCACCTACGG  94. CGCCGGACACGCTGAACTTGTGG  95.  2 out 34 35EGFP site 275 TTCAAGTCCGCCATGCCCGAAGG  96. GTCGTGCTGCTTCATGTGGTCGG  97. 3 out 35 36 EGFP site 275 TTCAAGTCCGCCATGCCCGAAGG  98.TCGTGCTGCTTCATGTGGTCGGG  99.  4 out 36 37 EGFP site  95GGCCACAAGTTCAGCGTGTCCGG 100. CGTCGCCGTCCAGCTCGACCAGG 101.  5 out 37 38EGFP site 203 CTCGTGACCACCCTGACCTACGG 102. CCAGGGCACGGGCAGCTTGCCGG 103. 6 out 38 39 EGFP site 463 CAGCCACAACGTCTATATCATGG 104.TGTACTCCAGCTTGTGCCCCAGG 105.  7 out 39 40 EGFP site  95GGCCACAAGTTCAGCGTGTCCGG 106. GCCGTCCAGCTCGACCAGGATGG 107.  9 out 40 41EGFP site  95 GGCCACAAGTTCAGCGTGTCCGG 108. CCGTCCAGCTCGACCAGGATGGG 109.10 out 41 42 EGFP site 101 AAGTTCAGCGTGTCCGGCGAGGG 110.CGTCGCCGTCCAGCTCGACCAGG 111. 11 out 42 43 EGFP site 350CGCGCCGAGGTGAAGTTCGAGGG 112. GCCGTCGTCCTTGAAGAAGATGG 113. 12 out 43 44EGFP site 174 CCGGCAAGCTGCCCGTGCCCTGG 114. CTTCAGGGTCAGCTTGCCGTAGG 115.13 out 44 45 EGFP site 100 CAAGTTCAGCGTGTCCGGCGAGG 116.GCCGTCCAGCTCGACCAGGATGG 117. 14 out 45 46 EGFP site 100CAAGTTCAGCGTGTCCGGCGAGG 118. CCGTCCAGCTCGACCAGGATGGG 119. 15 out 46 47EGFP site 101 AAGTTCAGCGTGTCCGGCGAGGG 120. CCGTCCAGCTCGACCAGGATGGG 121.16 out 47 48 EGFP site 107 AGCGTGTCCGGCGAGGGCGAGGG 122.CGTCGCCGTCCAGCTCGACCAGG 123. 17 out 48 49 EGFP site 155CTGAAGTTCATCTGCACCACCGG 124. GGCATCGCCCTCGCCCTCGCCGG 125. 18 out 49 50EGFP site 106 CAGCGTGTCCGGCGAGGGCGAGG 126. GCCGTCCAGCTCGACCAGGATGG 127.20 out 50 51 EGFP site  95 GGCCACAAGTTCAGCGTGTCCGG 128.GACCAGGATGGGCACCACCCCGG 129. 21 out 51 52 EGFP site 107AGCGTGTCCGGCGAGGGCGAGGG 130. CCGTCCAGCTCGACCAGGATGGG 131. 22 out 52 53EGFP site 337 CAACTACAAGACCCGCGCCGAGG 132. GCGCTCCTGGACGTAGCCTTCGG 133.23 out 53 54 EGFP site 337 CAACTACAAGACCCGCGCCGAGG 134.CGCTCCTGGACGTAGCCTTCGGG 135. 24 out 54 55 EGFP site 397GCTGAAGGGCATCGACTTCAAGG 136. CCTCGAACTTCACCTCGGCGCGG 137. 25 out 55 56EGFP site 100 CAAGTTCAGCGTGTCCGGCGAGG 138. GACCAGGATGGGCACCACCCCGG 139.26 out 56 57 EGFP site 101 AAGTTCAGCGTGTCCGGCGAGGG 140.GACCAGGATGGGCACCACCCCGG 141. 27 out 57 58 EGFP site 400GAAGGGCATCGACTTCAAGGAGG 142. CCTCGAACTTCACCTCGGCGCGG 143. 28 out 58 59EGFP site 337 CAACTACAAGACCCGCGCCGAGG 144. CTGGACGTAGCCTTCGGGCATGG 145.29 out 59 60 EGFP site 307 GGAGCGCACCATCTTCTTCAAGG 146.AGAAGTCGTGCTGCTTCATGTGG 147. 31 out 60 61 EGFP site 100CAAGTTCAGCGTGTCCGGCGAGG 148. CGTCGCCGTCCAGCTCGACCAGG 149. 10 out 61 62EGFP site 286 CATGCCCGAAGGCTACGTCCAGG 150. AGAAGTCGTGCTGCTTCATGTGG 151.10 out 62 63 EGFP site 337 CAACTACAAGACCCGCGCCGAGG 152.TGAAGAAGATGGTGCGCTCCTGG 153. 10 out 63 64 EGFP site 382GGTGAACCGCATCGAGCTGAAGG 154. CCTCGAACTTCACCTCGGCGCGG 155. 10 out 64 65EGFP site 275 TTCAAGTCCGCCATGCCCGAAGG 156. GCTTCATGTGGTCGGGGTAGCGG 157.11 out 65 66 EGFP site 349 CCGCGCCGAGGTGAAGTTCGAGG 158.GCCGTCGTCCTTGAAGAAGATGG 159. 11 out 66 67 EGFP site 382GGTGAACCGCATCGAGCTGAAGG 160. CTCGAACTTCACCTCGGCGCGGG 161. 11 out 67 68EGFP site 383 GTGAACCGCATCGAGCTGAAGGG 162. CCTCGAACTTCACCTCGGCGCGG 163.11 out 68 69 EGFP site 520 CAAGATCCGCCACAACATCGAGG 164.GATGCCGTTCTTCTGCTTGTCGG 165. 11 out 69 70 EGFP site 383GTGAACCGCATCGAGCTGAAGGG 166. CTCGAACTTCACCTCGGCGCGGG 167. 12 out 70 71EGFP site 415 CAAGGAGGACGGCAACATCCTGG 168. TCAGCTCGATGCGGTTCACCAGG 169.13 out 71 72 EGFP site 286 CATGCCCGAAGGCTACGTCCAGG 170.GTCGTGCTGCTTCATGTGGTCGG 171. 14 out 72 73 EGFP site 415CAAGGAGGACGGCAACATCCTGG 172. CAGCTCGATGCGGTTCACCAGGG 173. 14 out 73 74EGFP site 416 AAGGAGGACGGCAACATCCTGGG 174. TCAGCTCGATGCGGTTCACCAGG 175.14 out 74 75 EGFP site 101 AAGTTCAGCGTGTCCGGCGAGGG 176.GCCGTCCAGCTCGACCAGGATGG 177. 15 out 75 76 EGFP site 286CATGCCCGAAGGCTACGTCCAGG 178. TCGTGCTGCTTCATGTGGTCGGG 179. 15 out 76 77EGFP site 416 AAGGAGGACGGCAACATCCTGGG 180. CAGCTCGATGCGGTTCACCAGGG 181.15 out 77 78 EGFP site 417 AGGAGGACGGCAACATCCTGGGG 182.TCAGCTCGATGCGGTTCACCAGG 183. 15 out 78 79 EGFP site 524ATCCGCCACAACATCGAGGACGG 184. GATGCCGTTCTTCTGCTTGTCGG 185. 15 out 79 80EGFP site 106 CAGCGTGTCCGGCGAGGGCGAGG 186. CGTCGCCGTCCAGCTCGACCAGG 187.16 out 80 81 EGFP site 174 CCGGCAAGCTGCCCGTGCCCTGG 188.CAGGGTCAGCTTGCCGTAGGTGG 189. 16 out 81 82 EGFP site 186CATGCCCGAAGGCTACGTCCAGG 190. CGTGCTGCTTCATGTGGTCGGGG 191. 16 out 82 83EGFP site 417 AGGAGGACGGCAACATCCTGGGG 192. CAGCTCGATGCGGTTCACCAGGG 193.16 out 83 84 EGFP site 427 CAACATCCTGGGGCACAAGCTGG 194.CGATGCCCTTCAGCTCGATGCGG 195. 16 out 84 85 EGFP site 397GCTGAAGGGCATCGACTTCAAGG 196. GTCGCCCTCGAACTTCACCTCGG 197. 20 out 85

Surprisingly, the dCas9-FokI protein did not show detectable EGFPdisruption activity when co-expressed with any of the 60 gRNA pairs inhuman U2OS.EGFP cells (FIG. 5E). However, screening of the FokI-dCas9protein with the same 60 gRNA pairs did reveal EGFP disruption activityon target sites composed of half-sites in the PAM out orientation andwith spacer lengths of 13 to 17 bps and of 26 bps (approximately oneturn of the DNA helix more than the 13-17 bp spacer lengths) (FIG. 5B).Testing of FokI-dCas9 on an additional 25 target DNA sites with spacerlengths ranging from 10 to 20 bps and with half-sites in the PAM outorientation demonstrated efficient cleavage on targets with spacerlengths of 13 to 18 bps (FIGS. 5C-D). In these experiments, one siteeach was tested for spacer lengths of 17 or 18 bps and not all siteswith a 13 bp spacer length showed activity. Analysis of a subset ofsuccessfully targeted sites by T7EI analysis and Sanger sequencingfurther confirmed the presence of indels at the intended location. ThusFokI-dCas9 can be directed by two appropriately positioned gRNAs toefficiently cleave a full-length target site of interest. Forsimplicity, the complex of two FokI-dCas9 fusions and two gRNAs arereferred to herein as RNA-guided FokI Nucleases (RFNs).

To extend the initial findings with the EGFP reporter gene and toascertain whether RFNs could be used to perform routine genome editingof endogenous human genes, gRNA pairs were designed for 12 differenttarget sites in nine different human genes (Table 2). Eleven of the 12RFNs tested introduced indels with high efficiencies (range of 3 to 40%)at their intended target sites in human U2OS.EGFP cells as judged byT7EI assay (Table 2). Similar results were obtained with these same 12RFN pairs in HEK293 cells (Table 2). Sanger sequencing of successfullytargeted alleles from U2OS.EGFP cells revealed the introduction of arange of indels (primarily deletions) at the expected cleavage site(FIG. 5F). The high success rate and high efficiencies of modificationsobserved in two different human cell lines demonstrate the robustness ofRFNs for modifying endogenous human genes.

Example 2d. RFNs Possess Extended Specificities for Their Cleavage Sites

To test whether RFNs possess enhanced recognition specificitiesassociated with dimerization, whether these nucleases strictly dependupon the presence of both gRNAs in a pair was examined. In an idealdimeric system, single gRNAs should not be able to efficiently directFokI-dCas9-induced indels. To perform an initial test, two pairs ofgRNAs directed to two target sites in EGFP were used that had been shownto efficiently direct FokI-dCas9-induced indels to their target sites(EGFP sites 47 and 81) in human U2OS.EGFP cells (FIG. 5C). Replacementof one or the other gRNA in each of these two pairs with a gRNA targetedto an unrelated site in VEGFA resulted in reduction of EGFP disruptionactivity (FIG. 6A) and reduction of targeted mutations to undetectablelevels as judged by T7EI assays (FIG. 6B). Similarly, the effects ofusing only one of each of the two gRNAs were tested using pairs thatefficiently introduce FokI-dCas9-mediated indels in the human APC, MLHJ,and VEGFA genes (Table 2) and again observed loss of detectableRFN-induced indels by T7EI assay (FIG. 6C). These results demonstratethat efficient induction of genome editing by an RFN requires two gRNAswith appropriate complementarity to the full-length target site.

Given that the activities of our RFNs depend on the expression of twogRNAs, it was hoped that their mutagenic effects on known off-targetsites of one of the single gRNAs in the pair should be negligible.Performing these direct comparisons requires knowing the off-targetsites for a monomeric Cas9 nuclease guided by a single gRNA that itselfcan also serve one of the two gRNAs needed to target a dimeric RFN.Although very few monomeric Cas9 nuclease off-target sites have beendefined in the literature, five off-target sites had been previouslyidentified for one of the gRNAs we used to target the dimeric RFN sitein the human VEGFA gene (Example 1). Deep sequencing was used toascertain whether these five off-target sites showed evidence ofmutations in cells in which the VEGFA-targeted RFNs had been expressed(these are the same cells we used for the T7EI assay shown in FIG. 6C).The frequency of indel mutations at all five off-target sites wasindistinguishable from background (FIG. 6D and Table 3). These resultsdemonstrate that the use of RFNs can essentially eliminate theoff-target effects originally induced by Cas9 nuclease and a single gRNAand are consistent with our observation that a single gRNA expressedwith FokI-dCas9 does not efficiently induce indels. Although, atpresent, it is not possible to perform these direct comparisons onadditional sites such experiments will have to await the identificationof off-target sites for more single gRNA sites that can also target ahalf-site for a dimeric RFN, it was concluded that dimeric RFNs haveenhanced specificities relative to standard monomeric Cas9 nucleases.

TABLE 3 Endogenous Sequence SEQ SEQ of RFN target sites in Gene ID IDU2OS or 293 cells (spacer SEQ name left target sequence NO:right target sequence NO: sequence in lowercase) ID NO: APC1CCAGAAGTACGAGCGCCGCCC 198. TGGCAGGTGAGTGAGGCTGCA 199.CCGGGCGGCGCTCGTACTTCTGGcc 200. GG GG actgggcgagcgtcTGGCAGGTGAGTGAGGCTGCAGG BRCA1 GAATACCCATCTGTCAGCTTC 201. GGCGGAACCTGAGAGGCGTAA 202.CCGAAGCTGACAGATGGGTATTCtt 203. GG GG tgacggggggtaggGGCGGAACCTGAGAGGCGTAAGG DDB2 AATATTCAAGCAGCAGGCACA 204. CTCGCGCAGGAGGCTGCAGCG 205.CCTGTGCCTGCTGCTTGAATATTtc 206. GG GG cgccttttagggtgCTCGCGCAGGAGGCTGCAGCGGG EMX1 CCCAAAGCCTGGCCAGGGAGT 207. GCCCCACAGGGCTTGAAGCCC 208.CCACTCCCTGGCCAGGCTTTGGGga 209. GG GG ggcctggagtcatgGCCCCACAGGGCTTGAAGCCCGG FANCF- CCCTACTTCCGCTTTCACCTT 210. GGAATCCCTTCTGCAGCACCT211. CCAAGGTGAAAGCGGAAGTAGGGcc 212. site 1 GG GGttcgcgcacctcatGGAATCCCTTC TGCAGCACCTGG FANCF- CGCTCCAGAGCCGTGCGAATG 213.TGGAGGCAAGAGGGCGGCTTT 214. CCCATTCGCACGGCTCTGGAGCGgc 215. site 2 GG GGggctgcacaaccagTGGAGGCAAGA GGGCGGCTTTGG FES CGAGGAGACTGGGGACTGTAG 216.CCAGCTGCTGCCTTGCCTCCA 217. CCCTACAGTCCCCAGCCTCCTCGtc 218. GG GGccatgcctccgtctCCAGCTGCTGC CTTGCCTCCAGG GLI1 CATAGCTACTGATTGGTGGTG 219.CCGGCCCCTCCCCAGTCAGGG 220. CCCACCACCAATCAGTAGCTATGgc 221. GG GGgagccctgctgtctCCGGCCCCTCC CCAGTCAGGGGG MLH1 GGAAACGTCTAGATGCTCAAC 222.CAAAATGTCGTTCGTGGCAGT 223. CCGTTGAGCATCTAGACGTTTCCtt 224. GG GGggctcttctggcgcCAAAATGTCGT TCGTGGCAGGGG RARA1 CTGTTGCTGGCCATGCCAAGC 225.CCTGGGGGCGGGCACCTCAAT 226. CCGCTTGGCATGGCCAGCAACAGca 227. GG GGgctcctgcccgacaCCTGGGGGCGG GCACCTCAATGG RUNX TTCGGAGCGAAAACCAAGACA 228.GAGTCCCCCGCCTTCAGAAGA 229. CCTGTCTTGGTTTTCGCTCCGAAgg 230. GG GGtaaaagaaatcattGAGTCCCCCGC CTTCAGAAGAGG SS18 GGCCCGGTCGACTCCGGGCCC 231.TGCTGGGAATCAGCAGTGTTT 232. CCGGGCCCGGAGTCGACCGGGCCga 233. GG GGggcggaggcgggccTGCTGGGAATC AGCAGTGTTTGG VEGFA- GGGTGGGGGGAGTTTGCTCCT 234.TCCCTCTTTAGCCAGAGCCGG 235. CCAGGAGCAAACTCCCCCCACCCcc 236. site 1 GG GGtttccaaagcccatTCCCTCTTTAG CCAGAGCCGGGG VEGFA- GCCGCCGGCCGGGGAGGAGGT 237.GGCGAGCCGCGGGCAGGGGCC 238. CCACCTCCTCCCCGGCCGGCGGCgg 239. site 2 GG GGacagtggacgcggcGGCGAGCCGCG GGCAGGGGCCGG VEGFA- CCGTCTGCACACCCCGGCTCT 240.CTCGGCCACCACAGGGAAGCT 241. CCAGAGCCGGGGTGTGCAGACGGca 242. site 3 GG GGgtcactagggggcgCTCGGCCACCA CAGGGAAGCTGG sizes of cleavage SEQ SEQ DMSOThermo- amplicon products Gene primer ID primer ID added cycler sizein T7E1 name 1 used for T7E1 assay NO: 2 used for T7E1 assay NO:(yes/no) protocol (bp) (bp) APC1 GGCTGTGGGAAGCCAGCAAC 243.AAGCCAGGGGCCAACTGGAG 244. no touchdown 634 447/187 BRCA1GCGCGGGAATTACAGATAAAT 245. AGGTCCCATCCTCTCATACA 246. no touchdown 751454/297 TAAAA TACCA DDB2 ACCGCCCCTTGGCACCAC 247. CGGAGCTCATCTGCTTCCTGT248. no touchdown 627 456/171 EMX1 GGAGCAGCTGGTCAGAGGGG 249.GGGAAGGGGGACACTGGGGA 250. yes two-step 729 480/249 FANCF-GCCCTACATCTGCTCTCCCTC 251. GGGCCGGGAAAGAGTTGCTG 252. no touchdown 634361/273 site 1 CA FANCF- GCCCTACATCTGCTCTCCCTC 253. GGGCCGGGAAAGAGTTGCTG254. no touchdown 634 466/168 site 2 CA FES GGGGAGGGAGGCTCCAGGTT 255.GGCACAATGGCTCCCAAGCA 256. no touchdown 633 395/238 GLI1CCTTACCCCTCCCCTCACTCA 257. AGAAGGGCGGGCCAGACAGT 258. no touchdown 869590/279 MLH1 ATATCCTTCTAGGTAGCGGGC 259. TCTCGGGGGAGAGCGGTAAA 260. notouchdown 610 332/278 AGTAGCC RARA1 CCCAGGAAAAGTGCCAGCTCA 261.TGATGGTCACCCCAACTGGA 262. no touchdown 632 335/297 RUNXAAGGCGGCGCTGGCTTTTT 263. CCAGCACAACTTACTCGCACT 264. no touchdown 626389/237 TGA SS18 GGGATGCAGGGACGGTCAAG 265. GCCGCCCCATCCCTAGAGAAA 266. notouchdown 629 455/174 VEGFA- TCCAGATGGCACATTGTCAG 267.AGGGAGCAGGAAGTGAGGT 268. no touchdown 531 338/193 site 1 VEGFA-AGAGAAGTCGAGGAAGAGAGA 269. CAGCAGAAAGTTCATGGTTTC 270. yes touchdown 756482/274 site 2 G G VEGFA- TCCAGATGGCACATTGTCAG 271. AGGGAGCAGGAAAGTGAGGT272. no touchdown 531 288/243 site 3 Gene primer primer 2 used name1 used for deep sequencing SEQ ID NO: for deep sequencing SEQ ID NO.APC1 BRCA1 DDB2 CGATGGCTCCCAAGAAACGC 273. GCAGGTAGAATGCACAGCCG 274. EMX1FANCF- GCCCAGAGTCAAGGAACACG 275. AGGTAGTGCTTGAGACCGCC 276. site 1 FANCF-CATCCATCGGCGCTTTGGTC 277. CCGGGAAAGAGTTGCTGCAC 278. site 2 FESCTCCCCGTCTGCAGTCCATC 279. CCTGCAGGGACATGTGGTGA 280. GLI1 MLH1 RARA1 RUNXTAGGGCTAGAGGGGTGAGGC 281. CCGAGGTGAAACAAGCTGCC 282. SS18 VEGFA-ATGAGGGCTCCAGATGGCAC 283. TTCACCCAGCTTCCCTGTGG 284. site 1 VEGFA-ATGAGGGCTCCAGATGGCAC 283. TTCACCCAGCTTCCCTGTGG 284. site 2 VEGFA- site 3

Example 2e. Monomeric Cas9 Nickases Induce Higher Rates of Mutagenesisthan Single gRNA/FokI-dCas9 Complexes

As noted above, an important weakness of the paired Cas9 nickaseapproach is that single monomeric nickases can introduce indel mutationswith high frequencies at certain target sites (See Example 1 and Ran etal., Cell 154, 1380-1389 (2013); Mali et al., Nat Biotechnol 31, 833-838(2013); Cho et al., Genome Res (2013); and Mali et al., Science 339,823-826 (2013)). This lack of dimerization-dependence in the paired Cas9nickase system is a potential source of off-target effects because thetwo monomeric nickases can each create unwanted indel mutationselsewhere in the genome. It was hypothesized that because RFNs introducealterations using a dimerization-dependent FokI nuclease, these fusionsshould generally show less undesirable indel activity in the presence ofonly one gRNA compared to what is observed with monomeric Cas9 nickases.

To test this hypothesis, the activities of FokI-dCas9 and Cas9 nickasewere compared in the presence of a single gRNA at six dimeric human genetarget sites (a total of 12 half-sites; Table 4). These particular siteswere chosen because monomeric Cas9 nickases directed by just one and/orthe other gRNA in a pair could induce indel mutations at these targets.Using deep sequencing, the genome editing activities of FokI-dCas9 orCas9 nickase were assessed in the presence of both or only one or theother gRNAs. Both FokI-dCas9 and Cas9 nickase induced indels at all sixtarget sites with high efficiencies in the presence of two gRNAs (Table5). As hypothesized, monomeric Cas9 nickases directed by the 12 singlegRNAs induced indels with frequencies ranging from 0.0048% to 3.04%(FIG. 7A and Table 5). By contrast, FokI-dCas9 directed by the same 12single gRNAs induced indels at lower frequencies ranging from 0.0045% to0.473% (FIG. 7A and Table 5). Comparing these data directly, FokI-dCas9induced indels with lower frequencies than Cas9 nickase for 10 of the 12single gRNAs (FIG. 7A and Table 5). In addition, FokI-dCas9 showedgreater fold-reductions in indel frequencies than Cas9 nickase at 11 ofthe 12 half-sites when comparing paired gRNA rates to single gRNA rates(FIG. 7B).

TABLE 4 FokI-dCas9 tdTomato Indel tdTomato Indel FokI-dCas9 FokI-dCas9Frequency control tdTomato Frequency Chromosome Position Site IndelsTotal (%) indels Total (%) 6 43737290 VEGFA site 1 35000 150158 23.3087810 258108 0.00387 15 65637531 OT1-3 1 169681 0.00058 1 139847 0.00071 12131690182 OT1-4 4 190111 0.00210 5 139762 0.00357 12 1988060 OT1-6 3258976 0.00115 2 178162 0.00112 1 99347645 OT1-11 4 235853 0.00169 4186287 0.00214 17 39796322 OT1-30 1 261605 0.00038 1 286850 0.00034

TABLE 5 Deep sequencing of FokI-dCas9, Cas9n, and tdTomato controls at 6sites, with single and pairs of gRNAs (same data as presented in FIG.7). Nuclease Type or Control Site guideRNA Chromosome Position IndelTotals Percentages FokI-dCas9 VEGFA site 1 both 6 43737290 35000 15015823.3088 FokI-dCas9 VEGFA site 1 left 6 43737290 5 95476 0.0052FokI-dCas9 VEGFA site 1 right 6 43737290 9 91962 0.0098 FokI-dCas9 DDB2both 11 47236820 11303 50062 22.5780 FokI-dCas9 DDB2 left 11 47236820311 85726 0.3628 FokI-dCas9 DDB2 right 11 47236820 153 95050 0.1610FokI-dCas9 FANCF site 1 both 11 22647331 65846 195311 33.7134 FokI-dCas9FANCF site 1 left 11 22647331 19 27487 0.0691 FokI-dCas9 FANCF site 1right 11 22647331 845 225154 0.3753 FokI-dCas9 FANCF site 2 both 1122647138 27743 120314 23.0588 FokI-dCas9 FANCF site 2 left 11 22647138989 205832 0.4805 FokI-dCas9 FANCF site 2 right 11 22647138 142 1651300.0860 FokI-dCas9 FES both 15 91428181 14260 125912 11.3254 FokI-dCas9FES left 15 91428181 4 143877 0.0028 FokI-dCas9 FES right 15 91428181 7145495 0.0048 FokI-dCas9 RUNX1 both 21 36421217 61057 136164 44.8408FokI-dCas9 RUNX1 left 21 36421217 222 162636 0.1365 FokI-dCas9 RUNX1right 21 36421217 109 169122 0.0645 Cas9n VEGFA site 1 both 6 4373729014294 99036 14.4331 Cas9n VEGFA site 1 left 6 43737290 573 82316 0.6961Cas9n VEGFA site 1 right 6 43737290 315 101957 0.3090 Cas9n DDB2 both 1147236820 6673 31168 21.4098 Cas9n DDB2 left 11 47236820 1680 560192.9990 Cas9n DDB2 right 11 47236820 172 42424 0.4054 Cas9n FANCF site 1both 11 22647331 66827 193111 34.6055 Cas9n FANCF site 1 left 1122647331 1565 109029 1.4354 Cas9n FANCF site 1 right 11 22647331 2457109289 2.2482 Cas9n FANCF site 2 both 11 22647138 17007 111468 15.2573Cas9n FANCF site 2 left 11 22647138 120 100591 0.1193 Cas9n FANCF site 2right 11 22647138 1063 93162 1.1410 Cas9n FES both 15 91428181 16529126597 13.0564 Cas9n FES left 15 91428181 6 125196 0.0048 Cas9n FESright 15 91428181 23 46102 0.0499 Cas9n RUNX1 both 21 36421217 80029216800 36.9137 Cas9n RUNX1 left 21 36421217 1106 108670 1.0178 Cas9nRUNX1 right 21 36421217 2169 121413 1.7865 tdTomato VEGF site 1 none 643737290 29 313517 0.0092 controls (—) tdTomato FANCF site 1 none 1122647331 18 578378 0.0031 controls (—) tdTomato FANCF site 2 none 1122647138 81 393821 0.0206 controls (—) tdTomato FES none 15 91428181 21410620 0.0051 controls (—) tdTomato DDB2 none 11 47236820 14 1653140.0085 controls (—) tdTomato RUNX1 none 21 36421217 13 511977 0.0025controls (—)

The deep sequencing experiments also uncovered a previously undescribedand unexpected side-effect of certain monomeric Cas9 nickases: theintroduction of point mutations at particular positions within theirtarget sites. Cas9 nickase co-expressed with a single gRNA for the“right” half-site of the VEGFA target induced base substitutions atposition 15 of the recognition site at a frequency of 10.5% (FIG. 8A).Similar results were observed with Cas9 nickase and single gRNAsdirected to the “right” half-site of FANCF target site 1 (mutationfrequency of 16.3% at position 16) (FIG. 8B) or to the “right” half-siteof the RUNX1 target site (mutation frequency of 2% at position 17) (FIG.8C). Point mutations at these positions were not observed abovebackground levels in control samples in which no Cas9 nickase or gRNAare expressed in the cell (FIGS. 8A-8C). Interestingly, for two of thethree sites at which this hypermutation was observed, most of thesubstitutions observed are C to G transversions on the non-target DNAstrand. The positions at which these point mutations were observed fellwithin a strand-separated region of the target site that has beenobserved to be susceptible to P1 nuclease in vitro in adCas9/gRNA/target DNA complex. Importantly, these point mutations occurat much lower frequencies (five to 100-fold lower) in cells that expressFokI-dCas9 protein and the same gRNAs (FIG. 8A-C). Overall, it wasconcluded that FokI-dCas9 nucleases directed by a single gRNA generallyinduce mutagenic indel and point mutations with lower frequencies thanmatched single Cas9 nickases.

Example 2f. Dimeric RFNs Possess a High Degree of Specificity

Dimeric RFNs directed by two gRNAs are not expected to induceappreciable off-target mutations in human cells. RFNs, directed by apair of gRNAs to cleave a full-length sequence composed of twohalf-sites, would be expected to specify up to 44 bps of DNA in thetarget site. A sequence of this length will, by chance, almost always beunique (except in certain circumstances where the target might lie induplicated genome sequence). In addition, the most closely matched sitesin the genome to this full-length site should, in most cases, possess alarge number of mismatches, which in turn would be expected to minimizeor abolish cleavage activity by an RFN dimer. Indeed, all sites in thehuman genome that bear 0 to 16 mismatches (and that allow for spacers oflength 14 to 17 bps) for the 15 full-length sequences successfullytargeted with RFNs in this study were identified. This analysis showedthat all 15 full-length sequences were unique and that the most closelymatched sites in the genome ranged from 7 to 12 mismatches (Table 6).Sites containing this number of mismatches should not be efficientlymutagenized by RFNs and it will be interesting in future studies toconfirm this hypothesis. Overall, dimeric RFNs should possess a highdegree of specificity in human cells but the ultimate characterizationof specificity will await the development of unbiased methods that cancomprehensively define RFN specificity across the entire genome.

TABLE 6 Frequencies of candidate FokI-dCas9 off-target sites in thehuman genome that bear a defined number of mismatches Gene 0 7 8 9 10 1112 13 14 15 16 APC 1 1 2 16 74 414 2254 BRCA1 1 1 5 20 164 983 DDB2 1 27 58 267 1335 EMX1 1 1 2 8 40 175 828 3494 FANCF 1 2 4 44 298 1639 FANCF1 2 12 79 358 1718 FES 1 3 8 32 191 939 4505 GLI1 1 2 1 7 69 343 1711MLH1 1 2 5 22 96 643 KARA 1 1 2 8 39 187 698 2849 RUNX1 1 3 25 145 800SS18 1 1 2 6 39 280 1207 VEGFA-1 1 1 2 3 22 103 543 2676 VEGFA-2 1 4 999 447 1675 5608 18599 VEGFA-3 1 3 20 120 623 2783

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Other Embodiments

It is to be understood that while the invention has been described inconjunction with the detailed description thereof, the foregoingdescription is intended to illustrate and not limit the scope of theinvention, which is defined by the scope of the appended claims. Otheraspects, advantages, and modifications are within the scope of thefollowing claims.

What is claimed is:
 1. An RNA-guided FokI Nuclease (RFN) fusion proteincomprising SEQ ID NO:24.
 2. A nucleic acid encoding the fusion proteinof claim
 1. 3. The nucleic acid of claim 2, comprising SEQ ID NO:27. 4.A vector comprising the nucleic acid of claim
 2. 5. A host cellexpressing the fusion protein of claim
 1. 6. A method of inducing asequence-specific break in a genomic sequence in a cell, the methodcomprising expressing in the cell, or contacting the cell with, theRNA-guided FokI Nuclease (KEN) fusion protein of claim 1, and guide RNAsthat direct the RFN to two target genomic sequences.
 7. The method ofclaim 6, wherein the guide RNAs are: (a) two single guide RNAs, whereinone single guide RNA targets a first strand, and the other guide RNAtargets the complementary strand, and FokI cuts each strand resulting ina pair of nicks on opposite DNA strands, thereby creating adouble-stranded break, or (b) a tracrRNA and two crRNAs wherein onecrRNA targets a first strand, and the other crRNA targets thecomplementary strand, and Fold cuts each strand resulting in a pair ofnicks on opposite DNA strands, thereby creating a double-stranded break.8. The method of claim 6, wherein each of the two guide RNAs include acomplementarity region that is complementary to 17-20 nucleotides oftarget genomic sequence.
 9. The method of claim 6, wherein an indelmutation is induced between the two target sequences.
 10. The method ofclaim 6, wherein the two target genomic sequences each have aProtospacer Adjacent Motif (PAM) sequence at the 3′ end.
 11. The methodof claim 6, wherein the two target genomic sequences are spaced 0-31nucleotides apart.
 12. The method of claim 11, wherein the two targetgenomic sequences are spaced 10-20 base pairs apart.
 13. The method ofclaim 12, wherein the two target genomic sequences are spaced 13-17 basepairs apart.
 14. A method of increasing specificity of RNA-guided genomeediting in a cell, the method comprising contacting the cell with theRNA-guided FokI Nuclease (RFN) fusion protein of claim 1 wherein thespecificity of RNA-guided genome editing in a cell is increased comparedto genome editing with a native Cas9.